Prost was more sucessful because he had fewer DNF's in 1988-89. In that same period, there were only 6 races Senna finished in which he didn't win. As for McLaren "dominating" it was only those same two years that they were dominant. As the 90's arrived, Ferrari and then Williams especially had cars as good as, if not better than the McLaren.
In his years at Lotus, Senna was good enough to challenge Prost/ Mansell/ Piquet for the championship, even though their cars were better. Again, reliability is what let Senna down, and in 1987 he realised that although Lotus were good enough to drive him to a few Grand Prix wins, if he wanted to be World Champion he'd have to go elsewhere. Hence signing with McLaren and the rest is history.
Remember also that in his Benetton/ Ferrari years, Schumi had Ross Brawn on board, who is no slouch when it comes to operating within Formula 1. Also interesting to note that Benetton were never involved in allegations of cheating after Schumacher left, and subsequently there were plenty in the pitlane who had their suspicions about Ferrari's operations after a certain German driver joined them...
Prost scored more points than Prost while at McLaren. The aim of the game is to score points and win championships. Prost did better than Senna, when they theoretically had the same equipment. Of course, that was only theoretically as Prost will say that his treatment meant that he was actually given inferior equipment and treatment to Prost, yet he still beat him. I dont see how there is any way around this.
In fairness to Senna though, Alain Prost was one of the greatest ever. Who knows, maybe he was the greatest ever and better than both Shoey and Senna. But it is ironic, that the very things that people now accuse Schoey - Roughhouse and unsportsman driving tactics, dominant equipment, etc are exactly what Senna was accused of during his prime. In fact, i can recall Prost, in particular (and it is quite chilling hindsight) continuously calling for someone to step in and settle down Senna because he would kill himself or someone else if he kept driving the way he was.
Back to topic, i think that Shoemacher is the greatest based on his record. Prost may have been more consistent, Senna a little bit faster etc. But what Shoemacher has done with so many different teams, that started off as struglling for success and ended up as world champions, and then struggled for success after he left. It really is phenomenal. MClaren was the best in the world before Senna arrived. Bennetton wasnt, neither were Ferrari, but they both were when they left. Personally, i believe the only possible explanaion is that Schu gives first class effort off the field. ie he helps assemble the best crew and developers, and he gives them the best feedback to help them build the best packages. I think this places him above and beyond anyone else i have seen. On the track he is as good as anyone, but noone else is as successful with less dominant teams than Schumacher has been.
