I haven't been on these forums for a bit (too many things going on in my life, so much live D&D that doing it over the forums felt weird, etc) but I feel like I should chime in here.
I think people have noticed why I never tried to make a Tier system for PrCs. It's really hard, and there are far more variables than when dealing with base classes. Is the Mystic Theurge a good class? If it's advancing Wizard and Cleric, and the entry to it lost you 3 caster levels from each, then probably not. If it's advancing Sublime Chord and Ur Priest, then it's probably awesome... at some levels, but not at others. I'm not saying it's impossible to make it work, but it is quite difficult.
That last question of which levels you're playing at makes this incredibly difficult. With base classes it's a lot easier... if we're playing at level 5, we can discuss the relative power of Wizard 5 vs Barbarian 5, for example. But if we're playing at level 10, what level of Mystic Theurge should we be talking about? Wizard 3/Cleric 3/MT 4? Or is this a Sublime Chord/Ur Priest entry? Are we talking early entry? Likewise, classes like the Sublime Chord are awesome near the end of the progression, but Bard 10/Sublime Chord 2 is hardly interesting as a level 12 character, and is probably weaker than Bard 12. Issues of opportunity cost on entry mean that many PrCs are very weak early on only to become extremely powerful later, making it really hard to gauge what to call them. Again, not saying it's impossible, but there's a reason I didn't want to touch it.
I do think that the idea of rating by base class and then showing the modification is a decent idea, though it seems you'd have a lot of rankings (can you imagine the MT? Wizard/Cleric rating, Wizard/Druid with AT rating, Wizard/Druid without AT rating, Wizard/Archivist rating, Sublime Chord/Ur Priest rating... this will keep going for a while).
With that said, I will talk about the single most overrated PrC of all time, in my opinion: the Frenzied Berserker. Oh my god a Frenzied Berserker build can do 3000 damage on the charge! Wow! And yet, that same build, removing the FB and replacing it with more Barbarian, probably would have done 2000 damage on the charge. That's still enough to one hit kill any CR 20 enemy (they max out in the 800s, with most of them being in the 300s), so who cares? It's so easy to get insane melee damage anyway that 10 levels of FB often won't actually get you anything except for allowing you to kill things until they're even more completely dead. Meanwhile, now you have a chance of killing your party, and the usual melee issues (difficulty engaging targets, inability to do much except deal damage even when combat isn't the current challenge, etc) haven't been helped at all. Sure, you can deal with the "kill your party" issue, but doing so requires spending further resources (such as feats for Steadfast Determination, held actions for grease, whatever else), and you just haven't gained much. So yeah, I know the FB gives you really sexy damage numbers, but as far as actual usefulness in game play, I just don't see it. I'd rather have an Orc Fighter 4/Barbarian 16 with Headlong Rush, Power Attack, Shock Trooper, Spirited Charge, and a Valorous Lance than an Orc Fighter 4/Barbarian 6/FB 10 with the same, given the choice. There's just nothing the second character can do that the first can't do already unless your DM is actually throwing swarms of terrasques at you or you're well into epic, but that rarely comes up in most games (and at that point, it's time for the Wizard to shine).
Anyway, that's my thoughts on it.
JaronK