Psion said:
Translation: It can't do the impossible. Of course not. But there is no other system out there that even comes close to giving you such a nicely defined system for creating powers, effects, spells, etc.
I'm not talking about the impossible, I'm talking about character concepts and powers that other systems have no problem with.
Here are a few examples from the top of my head, which came up in our game:
Try to make a shapeshifter elegantly, and without costing 500 pts for only moderate capability.
Try to elegantly create a character who can summon black force which he can move and form into any shape, like Marvel's darkforce. This is a simple enough concept, but is a nightmare do implement. In the end I made it a power pool, and had to precalculate 6 or 7 pages of different effects.
Try to create a character who can freeze time, like in the time stop spell. For fairness he can't harm anything while time is frozen, but he can move objects or himself.
Try to create a character who can manipulate metal, and shape it into mechanical or mobile form.
These are superhero powers, but no doubt there are numerous spells in the PH that would be very difficult to implement as powers in champions. Polymorph other and shadow evocation and conjuration come to mind.
I'm not saying that the system is awful, because it most cases a power is relatively easy to convert into Hero terms, I'm just saying that because of the way the system works, many power concepts either become needlessly bulky and complicated, or cost way too much for what they actually do.
My group never used hero maker. Earlier I mentioned that the power system put off some players; this is true. However, I see nothing non-intuitive or especially difficult about the base system and I was able to run a fair cross section of players through it with little difficulty.
I played without heromaker for a while, but saw the light when I finally bought it.
The power system isn't what takes so long. Calculating costs, and figured characteristics, and determining costs for power frameworks and advantages with disadvantages, and so on, is daunting. Even the simple addition of all the costs can take a while.
I thoroughly disagree with that. Points are for players; as a GM you can just use the effects as a menu and pretty much do anything.
So it only takes 45 minutes to create a character, instead of an hour and a half. 
Besides, NPC creation wasn't only what I was talking about.
Imagine, for example, a situation where a huge Iron statue is rampaging, and is extremely tough to actually hurt. A character with fire powers and another with ice powers think up an idea where the fire character heats up the iron statue, the cold character then freezes it, and they repeat this a few times until a superstrong character then bashes the hopefully-brittle iron statue.
I as a GM like to reward this kind of quick creativity. However, by the Hero rules, each would be making completely seperate attacks, and the combination wouldn't do a thing unless they had previously bought it as a power combination. This kind of strict mechanical determinism bugs me.
If a player on the fly thinks of a new way he can use his power - not a new capability mind, but a new way the power he has always had could be applied - good for him. I like it when players think of novel solutions to problems, ones that I hadn't thought of and which are nevertheless completely within the capabilities of the character.
Another example from the same session was the fire character attempting to weld the statue to some Iron girders the character had lured it on to.
We see this sort of creativity in comic books all the time, but Hero doesn't reflect it well.
Granted, D&D's magic system isn't really great at this either, but I never said it was, and it isn't as important in fantasy as it is in the superhero genre.