Having played a MT, I can definitely tell you some of the weakness in 28 point 3.5 game at medium to high level with both a cleric and a wizard also in the party (currently 15th).
1st DCs for MT are going to be low. Creation points are split between Int, Wis, Dex, and Con. A pair of 16's cost you 20 of your 28 points. :\
2nd High level firepower is determined by the ability to deliver 2 spells per round. A MT has a lot of low level slots that are hard to use in combat. A lesser metamagic rod of quicken (expensive) is almost a necessity. Wizards and Clerics have a lot more high level slots that can be quicken.
3rd Delivering cleric attack spells is hard. Most of the better cleric attack spells are by touch. With Wizard like hp and ac, delivering attack spells by touch = death by 3.5 power attack. You have to either reach spell them (no harm for me) or spectral hand them (costs 1 rd of 5 for combat).
4th Buffing spells become less useful at higher levels. Most characters want to have Con, Str, buffed all the time. At 1 min. per level, the 2nd level cleric spells do not cut it for a high level game.
The MT ends up being a ranged damage dealer (low ac & low hp) that is weaker than a wizard in penetrating SR, lower DCs, fewer quickens, lower level spells (no horrid wilting), but with significant healing ability and flexibility (for that remove fear) in a 28 or 32 point game.
If however you let them go wild (40+ points or high rolls), then the limitations play less of a roll. The power of a MT would increase dramatically. Better DCs, better hit points, better ac, better init, etc. The same principle applies if you allow access to twilight/halfweight armor. The MT would be extremely weak in a 25 or 22 point game.
The MT works best when the party has neither a cleric or wizard, or the party already has one of each. The specialist is a lot better at filling their role than a MT. The MT is an interesting PrC because it is really balanced only in a certain range of stats.
-Psiblade