I agree that changing mex values should only be done with extreme care. It's such a fundamental building block of supreme commander that it will affect everything else. But one thing that always struck me as very strange is the lack of diminishing retuns when upgrading from T2 to T3 mexes. Consider:
Upgrading from T1 to T2 mex pays off for itself in 3min 45s
Upgrading from T2 to T3 and ringing it with mass storage pays off in 4min 17s
Cntr-k of a t2 mex, building a T3 mex and ringing it pays off in 3min 42s, faster than the T2 upgrade!
This contrasts massively with the very strong diminishing return of going from T1 to T2 mexes, or going from T3 mexes to Massfabs/RASboys. As a result, when being behind on the T3 eco upgrade, the window for punishing your opponent in the T2 phase is very slim, especially on the ever popular 20x20 team game maps.
Reclaim is a mechanic I think that has to be seriously looked at. It for sure increases the depth of the game in the T1 stage, but it is punishing the attacker increasingly as the game progresses. More often than not, a non-game ending land or navy push in the later stages of the game just ends up being a giant mass donation.