Naturally, any rule system can only be an approximation of the world (or theme/style) it tries to represent. There are cracks and holes, some big and some small, in any system. They are discrepancies between the game world reality and its mechanical representation. They are things such as only having 5 possible amounts of an attribute in the Storyteller system (when in fact Strength is much more variable), or having even stat numbers being more significant than odd stat numbers in D&D.
Min/maxers often exploit these little cracks in the walls to give their characters an edge. Naturally, it's a small edge - otherwise, we'd be talking about serious problems with the system - but it's an edge nonetheless. More notably, it's an edge which isn't justified in the game world.
The switching of systems, and conversion, naturally means a whole new and different set of cracks and holes. The same character, straightly converted, can't take advantage of them. Therefore, he is generally somewhat weaker.
In my opinion, the use of game-world approximation to make a character more powerful is metagaming and a bad thing, something to be avoided, something that doesn't fit my style of play; and if a side-effect of conversion is preventing the player from exploiting it, it's fine for me.
Then there is another, different problem. In 2E elven fighter/mages ruled. In 3E (barring PrCs) they mostly suck, managing to stay useful only with some very clever planning. Or consider two weapons fighting, or haste.
Unlike the previous issue, this is a real paradigm shift. The universe has changed, and being a mage and a combatant now doesn't work as well. Conversion, naturally, makes the character obey to the new universe. Which may make him substantially less effective, even if the player did everything as honestly and accurately as possible. This is because the character concept itself has been weakened, at a higher level than rules.
In these cases, the DM must decide how to operate the paradigm shift. Maybe a global catastrophe alters some magical/metaphysical laws, and certain people around the world get screwed as a result. Not good for the PC, naturally, but logical for the world.
More likely, the DM will just assume that everything has always been "new system style". Easier, faster, less messy. In this case, it would be fair to allow the player to alter the PC's concept during the conversion. After all, if the PC knew that being a fighter/mage would have never worked, he probably would have studied something different, or aimed for a PrC.
Even in this case though, I'm against giving the PCs arbitrary boons to allow their concept to work. If the DM and PC feel that the character absolutely must stay able to fight like a fighter and cast like a mage, they should realize that it's not just a matter of rules; it's a difference between the standard D&D world and their world. As such, it should be codified as a setting-specific rule and applied to PCs and NPCs alike.