If you don't like the bright thin sounds, you might want to try the classic Dimarzio SuperDistortions. The classic look is open cream colored humbuckers, but I ordered mine for a very few extra dollars, with a nickel cover. Some people use two of these. Others put it at the bridge and an Air Norton for the neck.
These SuperDistortions do not have ice pick highs like Seymour Duncan JB's can have, and they are EQ'd at the factory to be very powerful with strong mids and upper mids, with very tight but deep sounding bass. Great pickups. I suppose you would like them.
I also like Gibson '57 customs with the Plus bridge pickup. The '57 Custom pickup set has to be one of the nicest pickup sets ever made.
I have also read that the Custom Custom Seymour Duncan pickup goes well in SE's, along with the JB bridge pickup.
Personally, my next set of Seymour Duncan pickups will be either Antiquities, or other low output, old school, models like the Seth Lover. The Antiquities have aged looking nickel/silver covers similar to the raw nickel/silver pickup covers that I have installed on three of my SE's stock but unsightly zebra pickups with. You can brush these nickel/silver covers with a scotch brite pad to make them look, well . . . brushed. This is a very nice upgrade for like ten dollars total, if you like the stock pickups.
I dig the stock pickups in my SE Custom 24's and put the covers on them.
Don't be afraid to do a lot of adjusting to the guitar tone and volume controls to learn what the guitar already has in it for the tonal spectrum. You might be surprised.
What amp do you have by the way? Sometimes an amp upgrade will make your guitars really sound great. I bought a little Blackstar head, the HT5-RH, with reverb and it has the most beautiful almost three dimensional clean channel and an awesome drive channel - at very reasonable "stay at home player", cranked volumes with full tube saturation. It sounds just beautiful. There are a lot of great sounding amps that can add to you tonal options.
Good luck. I'd play the stock ones, maybe solder on some covers and mess around with the tone and volume knobs on your guitar and amp. The stock pickups are quite nice in my opinion - however, there are some really great pickups available, but it seems like you have to know what to order, unless you feel adventurous and want to just select ones that seem like they might be just right for you and try them.
I would advise to always "upgrade" your pickups, instead of downgrading them with some cheap imposters. I like to get premium pickups like Gibson, Seymour Duncan, Dimarzio, etc. Some other brands of course are also "known" to be super nice. I'd say though, that it is a good idea to do your research, like you are, and select some really nice upgrade pickups, if you find it necessary after playing around with these.