I agree with most of the responses here; 4e's changes to the skill system were quite welcome.
But I think OP is trying to get at something a little different, which is that (along with all the downsides) having lots of tiny little options allows for finer-grained differentiation of characters, making them seem in some ways more "real". Yes, in 4e you can (and should) do the joke-telling as a Diplomacy roll, but it means you normally won't see characters who are good at jokes but bad diplomats (or bad at jokes but good diplomats).
The oddities of skill clumping have been discussed before, and IMO if people really want a "solution", just let them (as part of a background, maybe, or even just on the fly) pick a few "sub-skill specialties" that go along with their character, so they can get a bonus on a particular usage. Like being a "swimmer" would give an extra +3 (feat bonus, to avoid abuse) to swim-related Athletics checks.
But I think OP is trying to get at something a little different, which is that (along with all the downsides) having lots of tiny little options allows for finer-grained differentiation of characters, making them seem in some ways more "real". Yes, in 4e you can (and should) do the joke-telling as a Diplomacy roll, but it means you normally won't see characters who are good at jokes but bad diplomats (or bad at jokes but good diplomats).
The oddities of skill clumping have been discussed before, and IMO if people really want a "solution", just let them (as part of a background, maybe, or even just on the fly) pick a few "sub-skill specialties" that go along with their character, so they can get a bonus on a particular usage. Like being a "swimmer" would give an extra +3 (feat bonus, to avoid abuse) to swim-related Athletics checks.