Here's my 2 silver.
I'll start off by saying that I like the d20 system. I've run it, more or less, since 3e came out. I am not a d02 hatter by any stretch (though I used to be before 3e).
That being said, I absolutely hate conversions of other games to the d20 system. This kills the uniqueness, IMHO, of the game. And, yes, the system is an intregal part of what makes a game unique.
Let's take the worst offender I can think of...Deadlands d20. Classic Deadlands was a brilliant piece of work. The mechanics, which included poker cards, poker hands and poker chips in addition to dice, made it have a sort of "Old West" feel. It made the game *different.* (For the record, yes, I have the same complaint against them turning Deadlands in to a Savage Worlds game)
Level systems are great for some games (like D&D or d20 Modern, or even Palladium), but for some games they'd just feel goofy, especially after playing the "pure" version of the game. Again, I point to Deadlands. And could you imagine trying to play the World of Darkness with levels? Or, gods forbid, Exalted? Part of the fun of a level-less system is that you really don't have a measuring stick for a creature or NPC's power level, or at least not a nice, neat one like a level system. The Players have more freedom because they are able to improved in the areas *they* want to improve in more readily. Rather than being limited by "level + 3" in a "class skill," they are limited by how much of their Bounty/XP/whatever they can pump into a skill.
So, for me, if it was a d20 game to start with (D&D, D20 Modern, Mutants & Masterminds, etc) great. No problems. If it wasn't a d20 game to start with, I vastly prefer the original system in every case that comes to mind, and I've played a LOT of different systems.