i like the guitar tonematch idea, even if it doesn't sound like my guitar with that pickup in it. what i have found is that there are magic combinations of guitar/pickups, and not every guitar will sound good with a certain pickup. for example: i have two 1986 Robin Wedges....there were only like 200 made, ever. of the 2 i have, one of them has stock pickups (that may be made by Schaller) and it sounds great for lead work. once upon a time, i took the pickups out of that guitar and put them in my other Robin Wedge (because the other one has a floyd rose) and those pickups sounded terrible in the other guitar. the smooth sounding Robin is made of basswood, the other is probably mahogany (judging from the dark tones) and needs a much brighter pickup like a bill lawrence or EMG to make it sound good.
with the tonematch that we are doing, i can chose a complete guitar that works with a given amp and wail away. i used my Charvel with EMG'S to play this morning, and the tonematch i used was an Eric Johnson strat. i played through the Plexi model and you would have thought i was Lincoln Brewster with the tone i had.
instead of thinking that the tonematch has limitations; i consider the limitations to be a plus....i would much rather have the tone of a great sounding guitar than to have those same pickups on my crappy sounding body wood.