SEED is the only Gundam series I have liked from what I have seen. V, Wing, SEED. Gundam 00 I am not touching that with a 100ft pole. V contains all sorts of retarded. Wing is super robot with liberal doses of Bullshit.
Mechs in SEED does have proto-types (Original 5) and what not. There is a clear line of evolution with most of the mechs (Not so much for Freedom, Justice, Providence).
Of course for some form of realism one would like to see their Mechs evolve over time(variants, extra equipment etc), however, do it too many time and fans start bitching that the show just wants more model sales. You really can't win. (A charge thrown at GSD)
As long as a series doesn't move towards way or the other over time (Betraying it's own premise) it's ok to mix elements from both schools of robot. SEED does this successfully, where a lot of other don't including most of it's related series. SEED was quite frankly a return to the series' roots with updates and a modern look.