When was the last time a non-factory rider won a MotoGP race? Any MotoGP fan worth their salt will be able to give you year, track and rider: 2006, Estoril, Toni Elias. Ask them why he won and they will give you all sorts of answers – Dani Pedrosa taking out Nicky Hayden in the early laps, Colin Edwards not being able to maintain his pace to the end of the race, Kenny Roberts Jr misjudging the number of laps left in the race, or, as Valentino Rossi put it, because 'Toni ride like the devil' – but none they can be sure of.

There is a less well-known explanation for Elias' performance, though. Ahead of the Estoril race, Elias was given a set of the overnight special tires shipped in especially for Michelin factory riders. In this case, Elias was handed a set of 'Saturday night specials' destined for Dani Pedrosa, but which Pedrosa had elected not to use, and so were going spare. Elias liked the same kind of soft carcass tire which Pedrosa was being offered, and went on to exploit the advantage it offered.

What does that have to do with Friday at Qatar? Two things. Firstly, it highlights exactly how important tires are in motorcycle racing. Tires dictate a huge amount of the performance of a motorcycle. They are the connection between the bike and the track, but that is a very full and complex function. Tires determine how far a bike can be leaned, how much drive the bikes can get out of a corner, how well the power delivery of an engine transfers to the tarmac, how hard the bike can brake, they provide a certain amount of suspension, and they pass information about track surface, grip conditions and where the limits of braking and turning are for a motorcycle. And that's just the beginning. Tires are (quite literally) a black art. Their complexity cannot be underestimated.

The importance of tires leads onto the second point: the importance of equipment. Different riders have different tires, and their results differ because of that. This was true in the past when some riders were given tires built specifically to their demands, while others were forced to make do with the standard tires the tire companies had brought along as standard issue. Similarly, different riders have different bikes, and their results are not the same. A long time ago, the massive difference between satellite bikes and factory machinery meant that riders on a satellite bike didn't really have a chance. Today, that gap is smaller, but there are still important differences. Alvaro Bautista's bike is very close to that of Dani Pedrosa's, but he has to run Showa suspension and Nissin brakes for contractual reasons, and without the massive development which Öhlins pours into MotoGP, progress for Showa and Bautista is much slower. There is little doubt that Dani Pedrosa is a more talented rider than Alvaro Bautista, but some of the difference is in forks and brakes.

Back to Qatar. There are howls of indignant rage both inside and outside the paddock, complaints about the new rules and the different tire options available. It's not fair that we only have 20 liters of fuel, the Yamaha men cry. It's not fair the Open class riders have the soft tire, the satellite riders cry. It's not fair that the factory riders didn't get to test at Qatar, the fans cry – and as the factory riders have the largest contingent of fans, their cries are heard loudest, on social media and on forums.

While there is some merit in their complaints – the rules are a bit of a mess, a necessary evil which has finally helped persuade the factories to adopt spec electronics from 2016 – the accusation that it isn't fair misses the point. The rules were set last year (with the exception of the chaotic last-minute adoption of a special rule for Ducati) and the factories and teams made their various decisions about which avenues to pursue. Honda and Yamaha knew that they would have a liter less fuel, and Yamaha knew that fuel consumption was always a problem for them. Yet Yamaha accepted Honda's proposal, and decided to remain as a Factory Option team, rather than switching to the Open category and taking the extra fuel. They knew the challenge they faced, and they accepted it willingly.

Of course, it is the riders who suffer the consequences of Yamaha's decision. Valentino Rossi has been struggling with fuel almost since the start of the 800cc era, when the allowance was reduced to 21 liters. The reduction to 20 liters is killing him at a track like Qatar. He describes the engine as running on air, the bike having no power out of the last corner and along the straight. Ironically, Rossi is posting top speeds of 336 km/h along the straight, 5 km/h slower than Marc Marquez, and 6 km/h slower than the fastest Ducatis, but still nearly 11 km/h faster than Aleix Espargaro on the Open class Yamaha with 24 liters of fuel. And it is Aleix Espargaro who has topped the timesheets in all three sessions, and leads the way going into qualifying.

While Jorge Lorenzo has fewer concerns about the fuel, he is seriously worried about the rear Bridgestone tire being used at the moment. He once again branded the tire as dangerous, and brought the subject up in the Safety Commission, where the riders sit with representatives of the series to discuss matters of safety. While Lorenzo has little backing for the claims that the rear Bridgestone is dangerous, the other Yamaha men all back his complaints about the tire. The 2014 tire is basically the same tire that was used at Assen and Mugello last year, one which includes a heat resistant layer. It works superbly at tracks which stress the tires, but in the dusty and cool conditions at Qatar, the heat resistant layer merely robs the tire of edge grip. Lorenzo's style in particular relies on being able to generate edge grip as he spends a long time leaned right over and carrying corner speed.

The tire is also posing problems for the Tech 3 riders, though it is not slowing them up much. Both Pol Espargaro and Bradley Smith suffered big crashes, though both came away relatively unhurt. Smith described his crash as a '500 crash', a massive highside reminiscent of the 500cc two-stroke era. His crew had sacrificed a little bit of edge grip for a bit more mid corner speed, and Smith paid the price. The lack of edge grip for the Yamaha men clearly making set up more critical than it was last year.

Real improvement will only come at Le Mans, when Bridgestone will bring a modified version of its medium compound 2014 tire for the rest of the season. That modification will use technology applied to the hard tire at the end of 2013, which provided more edge grip and turned the harder option tire from a garage ornament into a viable race option. Though the modified tire probably won't provide the same feel at the cooler and less grippy tracks that last year's tire did, it will surely be an improvement on what they have now.

The combination of fuel and tires is not the only reason the grid order has been shaken up. The fact that the satellite and Open class teams all tested here two weeks' ago is also still having an effect. But that effect was diminishing in every session: while the riders who had tested here all took a half a second off their times from yesterday, the factory riders, who had been testing tires at Phillip Island instead of Qatar, improved by well over a second. Marc Marquez has moved up the order to fifth, and all of the factory riders bar Cal Crutchlow made it straight through to Q2 by the end of FP3.

For Qatar remains a strange track. The low grip conditions require a lot of confidence to learn to trust, and that only comes with track time and set up. Satellite riders and teams have that, the factory riders don't.

Which means we have a rather fascinating prospect for qualifying. Aleix Espargaro and Andrea Iannone, the two riders who most often found themselves having to battle through Q1 to get into Q2, now top the timesheets and qualify on merit. However, the rest of the riders going through to Q2 are those you might expect: the top 12 consists of Aleix Espargaro and the 11 Factory Option riders. The order may be a little less conventional, but some of that is surely down to testing. If all of the riders had tested at Phillip Island or Qatar, the order may have looked a little different.

Aleix Espargaro's domination of the timesheets – his odds to win halved again after today, now down to 5/1 from 11/1 yesterday, and 51/1 before the riders had hit the track – has been much talked about as being a sign of how the rules are unfairly affecting the standings. But Repsol Honda team principal Livio Suppo was much more candid about the situation. When asked about how poorly the Honda RCV1000R was performing compared to the Forward Yamahas, Suppo was clear: 'Our problem has a first name and a last name: Aleix Espargaro.' It is Espargaro's performance which has raised eyebrows, but his speed has more to do with his ability than the bike he is on. Spending years on different bikes, few of them competitive, teaches you a lot of things about managing a racing motorcycle, and now Aleix finally has a chance to put all those to use.

Where the rules will have the biggest effect is during qualifying. The softer rear tire the Open class bikes and the Ducatis have is a genuine advantage, and is likely to produce a few surprises on the grid. Aleix Espargaro looks to be the hot favorite for pole, the Forward rider fast on both the soft and the medium tire. The Ducatis, too, are benefiting, with the exception currently of Cal Crutchlow. Andrea Iannone and Andrea Dovizioso were 2nd and 4th overall, and should both find slots on the first two rows tomorrow. Apart from them, it seems more likely that normal service will be resumed, with Marquez, Lorenzo, Pedrosa and Rossi all picking up speed.

The softer tire is playing out much as expected, acting much as the old-fashioned qualifying tires did back before the single tire rule. Back when there was a super-soft qualifier, a brave rider could earn a starting position much closer to the front than his race pace deserved, adding some interest and excitement to the first part of the race. It looks like something similar will happen with the Open class softer tires, with the Ducatis and Aleix Espargaro capable of seriously threatening for pole.

Once the race starts, the situation may be a little different, with quality coming to the fore. That won't stop Aleix Espargaro though. Aleix set his fastest time on the super-soft tires he has at his disposal, but he was still the fastest man on track on the medium tires (hard for the Open class, soft for the Factory Option class) which everyone will be racing on. Valentino Rossi tipped Aleix as the favorite for the pole. Looking at it on Friday, you'd have to say he's favorite for the race as well.