Honda definitely favoured Senna with more powerful engines.
McLaren did not know of this, Honda were always very secretive. The favourtism was strongly denied, honestly by McLaren...
Prost knew it immediately from their time-traces, lap times and saw it on-track, the way Senna pulled away from him exiting corners.
From being 0.3 slower than Senna on best, pre-race time, season-average for 1988, Prost was suddenly 1.0 down in 1989. As Alain said: "No way is a driver suddenly a second slower than his team-mate!"
Prost got confirmation about this favouritism years later when he had lunch with one of the Honda engineers and made sure the guy had quite a lot of liquid refreshment.
This is interesting...
I agree Honda or somebody did favour Senna in 1989 as the performance gap was much larger.
However, a much overlooked fact is a change in regulation to do with minimum weight. I believe this came into effect in 1989.
Prost was 10kg lighter than Senna and the minimum weight regulations were only for the car and not car and driver before 1989. Thus lighter drivers had quite an advantage.
They then made it car + driver for minimum weight to even it out more. Lighter drivers still to this day have an advantage as they have more ballast to play with, however no where near the advantage of the 70s/80s
Even with what you say, losing almost an entire second as someone suggested, is not plausible. You not only can up ballast, but instead put more fuel in... burn more when needed. It all depends on the car, weight and its distribution and what else have you. Whichever way you cut it, Prost was still in a better position compared to Senna with what you say, and i'm willing to bet my kidneys (yes, both!) that Prost wasn't so slow, as you're perhaps inferring. I don't know if you read a story about a young Prost sandbagging... can someone link it please?http://www.grandprixhistory.org/ramble5.htm
anyhoo, for want of a better source, here's a link for those who want more to find on Prost (well, for free that is)...