What sound are you going for? What don't you like about the stock pickups?
I could suggest HB sized P-90s, or Filtertrons, or Duncan Invaders - since I don't know what you're after.
Hard to go wrong with USA PRS pickups, like 57/08's or 59/09's
Lots of good Duncans and DiMarzios out there.
Suhr Aldrich set and Bare Knuckles are often recommended.
I've used several Duncans in various guitars including Jazz, JB, '59, and Alternative 8, and each has its' virtues.
Sorry, I'm being a smarta$$, but your question is too vague.
The above is absolutely correct.

My favorites are 59/09 followed by SD Jb/jazz or 59 in the neck. One of the SD customs in the bridge is an excellent choice for the bridge instead of a JB too. I've never owned a pair of 57/08 but have played them and on my list for a guitar one day. I really dig my DW tomahawks for a unique pickup that sounds very different depending how you set it up or play. The Metals ate another one on my wish list that have very high prsise.
Interesting question, how are you going to install it?

Its a simple install with s screwdriver, soldering iron, and wiring diagram. Take pictures of the connections before you remove them for reference if needed. A multimeter is helpful too.
It depends on what you're going for tonally.

ie- some of the pickups I have are voiced in a way to lend themselves better towards some applications better than others. As much as I'm a sap for Bare Knuckle pickups, they're each geared towards something I'm trying to go for tonally. My '11 Custom 24 has a Painkiller set that lends itself well to clarity under lower tunings and an aggressive mid spike to help them retain clarity under gain. My '08 Custom 24 has a Holydiver set that's clear, but comes across as more of a thick, saturated wall of sound under gain.

Here's a couple sample clips of both to hopefully better illustrate the aforementioned:

'11 Custom 24 with Painkiller set

'08 Custom 24 with HD set
I replaced the HFS/VB's with 85/15S's and put in a custom wiring harness. But, that is what I like, you may feel differently. This is a difficult subject to answer without knowing all the details of why, and what.
I replaced the HFS/VB in my S2 with 57/08’s. There was nothing really wrong with them, but I tend to like lower output pickups. I changed the 496/500 set in my LP for a set of T-Top replicas also. I’m just not capable of taming those higher output pickups. I will say, the HFS was very clear on a clean amp and I preferred it over the VB in that aspect.