I have thought of one problem with this idea, although I am fully an advocate of it.
It is all fair and good if you change engines or MTOW on a B737 or A320 because it will still be a B737 or A320.
However, if you change MTOW on, say, and E175STD its increased range would make it an E175LR for example. As far as the game goes this is completely a different plane and would effect global statistics of planes, is it really possible to change what the aircraft is in this way. It would change aircraft value, generally increasing it for the longer range variants.
Another issue is, say to increase the range of an MD81, it is not just an MTOW change but also changes the engines to uprated ones, for it to become an MD82 or MD83. If people could do this upgrade it could lead to people abusing the system because we know when the planes are released, they order a load of MD81s and then instead of converting orders they just change them when they are delivered as an extra maintenance action.
My final example is, say, to keep engine commonality on Airbus A300B2, you change all the Pratt and Whitney engines to General Electric, then your aircraft will be changing from A300B2-120 to A300B2-100. However I believe these aircraft could be condensed into just the Airbus A300B2-100, A300B2-200, A300B4-100, etc and each has two engine choices.
Because no other airbus has the designation changed for engines, only the A300. e.g. the A380 is always an A380-800 in game, not A380-860 or A380-840 depending on engine choice, so it is wierd because the A300 is the exception. Plus is looks messy in my opinion having so many different A300s.