At least in my experience, there has been a drop in custom spell research (by PCs, at least) in 3e games, and it seems largely due to a shift in the default pacing of the game. In the 2e Forgotten Realms game I ran, the players generally controlled the pacing of the game...they went out exploring when they had some spare time or needed money, and took time to research spells or craft items as appropriate. (There were enough Harpers and other NPCs around to handle lesser threats, and big threats generally took time to come to a head...the BBEGs needed time to prepare, too.) At the higher levels they weren't levelling very quickly even when actively adventuring, so researching new spells tailored to their specific circumstances was a productive use of time.
In the 3e Greyhawk campaign I'm currently playing in, events transpire very quickly...there are always several villainous schemes afoot, and neglecting to follow up on them leads to dire consequences within a week. Admittedly much of this is due to a difference in DM style, but a major contributing factor is the pace of levelling...our characters are well into epic levels, and we still manage to level once every few days when actively adventuring. Given that our opponents are assumed to progress at the same pace, taking weeks off to research even one mid-level spell can put us at a crippling disadvantage. There are custom spells in the game, but they were all developed by NPCs (who either researched them during a rare period of boredom many years ago, or were ordered to research them by a boss in whatever organization they belong to).
The epic rules, if in use, even further discourage normal spell research. Why would you spend 45 days researching a 9th-level spell when you could research an epic spell in 5 days or make a 9th-level Pearl of Power in 9 days using Efficient Item Creation? Yes, those activities cost experience, but the rapid pace of levelling ensures that you can gain the necessary experience in just a few days. There is a list of spells that my wizard would love to research, and some of them are in fact already written out in detail and have DM approval, but my character simply hasn't had time to research them...