You had 44 homebrewed prestige classes in 3e? Wow. That seems HUGE to me.
Yeah, frequenting ENWorld ends up provoking my creativity in a ton of ways. Some of those were a new category of prc based on racial paragon classes- cultural paragon prestige classes, where you could take a 3-level path that added a number of features emphasizing things tied to the culture you were from (separate from race). Then there were a few that were made to emulate old kits, or to put a new spin on organizations in the campaign, etc.
I'll agree that it's probably more than most had.

But I've always been one of those "spend hours on my campaign" types of DM, and in 3e, that led me to make tons of custom feats, prestige classes and feats, both for the pcs (some were even aimed at specific characters) and for my monsters and npcs.
Mostly things were made up when there was not an acceptable equivalent to do a specific thing already, and most homebrews were dropped due to lack of use, overpowered, underpowered, or otherwise just fell out of practice.
While not all that homebrewed material of mine got used by any means, the players loved having all those options in front of them. When I found something was broken- either over or underpowered- I'd revise it. I hated doing it if someone was using a feature, and would always offer the option to back out of changed material if the pc wanted to, but there were almost no options that I ended up completely dropping.
Now, on the 4e side. In the few games of that I ever saw (or joined/asked to join) there were many little changes. Mostly when people were swapping powers from one class to another - even then nothing particularly new was created. But, I do admit it was more common.
Interesting. I would have thought 4e homebrewing to be less common due to the difficulties a lot of people seem to have in making a pc without the CB. (Caveat: I never really understood why this is so hard, other than the amount of writing powers down that you need to do.)
Never saw 4e's epic destinies in play, but from what I remember I suspect the numbers for that one might be higher if only by design - you are EXPECTED to make things up for your character, something unique; though again every time I heard of 4e epics they sounded fairly similar (if not exactly the same) as what was in the book - something I thought was a little disappointing.
Yeah, epic levels are ripe for total customization IMHO. The same held true in 3e; if you had an epic axe-wielding dwarf fighter, by God, you ought to have some custom epic axe options (IMHO and IMC)!
I had a hard time coming up with new 4e EDs until we got pretty close to epic and I began to cotton to what 4e epic play ought to look like. Now I've got a bunch tied tightly to the campaign, and like you said, several of them were made with pcs in mind (even if they don't all end up getting taken).
But yeah, that "tied tightly to the campaign" bit is the key to much of my custom stuff, from 3e prestige classes like the mist pirate or mystic chef, to 4e material like my "alpha mutant" epic destiny- my preference is to make stuff you won't find in the books because the background material isn't there (the Isles of Mist, my halfling food-based culture in the campaign, my radiation rules).