Neither of them were half as good as Schumacher and he alone left them no chance of winning the WDC. It's a completely different situation with Alonso and Raikkonen.I think you are wrong. Ask Rubens Barrichello or Eddie Irvine.
It's easier to create/develop a car for a team with a lower budget earlier in the season because the FOM prize money rolls in in December. As the year goes on, the money runs out (for Lotus, that apparently happens in August, at which point Genii has to start financing them) and development slows down. For the bigger teams that doesn't happen.You did not create better car by magic. They just did better job (also comparing their resources) and thats it.
Also, we all know why McLaren started out with a bad car this season. They took a risk and fell on their noses. It's an exception and hardly serves as a good example.
For further info on Lotus' finances: Auto Motor und Sport (German magazine) released an article about it. Unfortunately, the Google translate version of it is kinda horrible :-/