You've got it bass ackwards
You need to step back and look at the problem as a whole. No rider is gonna turn round and say, hey, I think we need a V5 motor. The rider is gonna say, hey we need more power but without losing torque and driveability. The engineer is then gonna turn round and say, hey maybe we should be looking at a V5 motor. And then if he has a factory behind him that trusts what both the rider and the engineer are saying, the motor gets produced. So although the rider has no say in exactly what gets produced, it is his direction and needs that are met by whatever the engineering department provide as a solution to a particular problem, whether it be an engine configuration, or a carbon frame.
I'm sure this was true of Rossi and Yamaha. Rossi didn't get out of bed one morning, pick up his phone and say, Jezza! I think we need a crossplane crank. No, he would have been asking for an engine that drives well out of corners, goes up the straight like a stabbed rat, and dosen't chew up tyres. Infact as I recall Furusawa had 3 different engines for Rossi to choose from before the 04 season. Furusawa as an engineer obviously felt that a crossplane crank could produce what a rider needed, but what works on paper dosen't always work in the real world. Rossi chose the engine with the crossplane crank, despite not being the fastest in a straight line, and thats what Yamaha ran with due to Rossi's direct intervention. Had Rossi chosen differently, then we would never have heard of it.
As someone else has stated on this thread, succesful racing is a team sport, which is absolutely right. You need to have a talented rider who can give accurate information and have an understanding of what the bike is doing. This is the hardest part. There are no guages or instruments to measure how a bike feels to a rider, its all down to experience, instinct and pure talent. You need a competent chief engineer to translate the needs of the rider into an engineering solution, and you need to have a race department in a factory that trusts the rider and engineer, and that has the impetus and skill to produce what is being asked for. To achieve success at the level of competition we are currently seeing in Motogp, all of these elements must be in place. But as I have stated before, the initial direction must come from the rider.
With regard to Suzuki, you're right, they're not throwing the resources at it. And I think the reason they are not doing that is because they know it'll be a waste of money. And thats because without a top drawer rider to give top drawer direction they have no hope of success. Once they have that they need a top drawer Chief engineer, and then a factory with the money and impetus (do you feel like you've been here before?) to produce what is being asked for. But it all starts with the rider.
You only need look at Honda to see what happens when development philosophy is factory led. Honda have the engineering skill and money to produce race winners. But because they don't look to their riders for direction (probably because the quality of information is so variable) they haven't won a championship since 06. Having said that it looks very possible that they could win this year, but look how long its taken someone as big as Honda to get it right. Then by comparison, look how long it took Yamaha to turn things around at the end of 03. Because they listened to their rider first and foremost