get that bridge pickup real close to the strings and come back a little if it sounds like built in tremolo effect - a little may be ok.
That is where P90's come to life.
I know you're right, and my junior does have the P90 very close to the strings; sounds amazing. But, there are two issues with that on the Epiphone: 1) The screws are not long enough to get the pickup any higher (and the bridge can't come down any lower either; the truss rod is maxed out which is rather worrying...); Epiphone seem to have unusual pickups when compared to Gibson insomuchas they have more output (too much?) and can easily sound harsh and compressed - thus, Epiphone pickups sound good a bit further away from the strings than a Gibson pickup would, imho - if you watch the Anderton videos, the Lee fella often makes a similar point about Epiphone pickups - they just sound a bit nasty at times in a way a Gibson/Lollar/Bare Knuckle wouldn't, and a solution is to have the pickups a bit lower.
At the current heights, the Epiphone pickups sound sweet and have some oomph that a P90 should have - in the punky space, would drive a fuzz pedal perfectly (the junior doesn't need a fuzz pedal, it can drive an amp there by itself). They do lack the snarl of the junior (and that is at least in part due to the pickup height, exactly as you said), but I have the junior when I want that, so the guitars are differently voiced which suits me fine.
So, in a long-winded way, I'm kinda saying that I know you're right, but on this guitar with these pickups with the jnr in my arsenal, the pickups will probably stay at their current heights.
To big up this little Epi again, as a bit of a Gibson fanboy who isn't fond of the Epiphone brand much, this little Yellow Monster gets you a fair amount of Gibson-ness for $420. I've always been of the opinion that a low end Gibson LP is far better than a high end Epiphone LP (although I accept other folks with the opposite opinion may well be right for them), but I was thinking yesterday if I'd prefer this guitar or a Gibson double cut tribute special which is double the price - I'd have to try the Gibson out for sure, but even at the same money I might go for this Epiphone (now I'm being silly...) because it looks and feels right; frankly, I'm surprised that an Epiphone can play this well - the neck is very good.
Not expensive, $10 for 4 - worth it for the looks, similar to the stuff Dave suggested, but slightly more tonal space because I noticed not much tonal difference with the current knobs (not bad, but would like a bit more sweep), so if the cpas don't do it then I'll now we need pots at some point.