I was looking at these two models...
Agile AL-3000 HSB- http://www.rondomusic.com/al3000mhsb.html

Or the Epiphone standard in the Transparent honey finish- http://www.musiciansfriend.com/product/Epiphone-Les-Paul-Standard-Electric-Guitar?sku=518341

I want them for Guns N' Roses, Metallica, clean stuff, classic stuff, metal stuff. An all around guitar pretty much.
I will change the pickups in either one with GFS pickups.
This in the bridge... http://store.guitarfetish.com/crpafhiouhuz.html
This in the neck... http://store.guitarfetish.com/v59clalpazeh.html
And make them both Splittable using push/pull pots.

So the Epiphone or the Agile, and are the pickups I chose good for what I play?
I've heard decent things about Agile, but personally I would go with the Epi. I'm really happy with mine, quality was good, played great and it really shined with a pickup change.

For the pickups though I'm not sure I would go with GFS, I've heard some pretty "meh" things about them. If you have the cash maybe toss a Duncan '59 in the neck and a Custom 5 in the bridge. That should give you plenty of versatility. Although I would hold out on pickups until you upgrade your amp first.
So long as you can try the Epi out in a store first, go with that.

Epi have weird quality standards, so it's a bit random how good any given instrument from them will be: some are amazing and on-par with higher-end instruments, while many are average, and some are utterly awful.
Obviously if you order a guitar in via a store or online, there's no way you can tell what you're going to get. The guitar that is sent might be great, but the chances are it'll be average, or worse, you might get one of the rubbish ones.
So, only buy the Epi if you can get to a store, and try a bunch of them out, and cherry-pick the very best one you find. Don't just settle for an average one, you'll regret it in the long run. If you can't try them out in-store, or if a store only has one or two to compare, then don't bother, go with the Agile.

I've got an Epi LP Custom that I spent about a month finding a good one, I upgraded it's pickups and changed the bridge, now it's better than one of my Gibsons. However, if I hadn't been able to spend the time trying out a ton of them to pick the very best one, I'd have much rather have bought something like an Agile.