Hm. I don't do either, anymore, except for one digital card game, but I was a tournament player in both for many years. I think minis games provide more depth of enjoyment, just because of the time involved to construct an army and paint it. I always created a background and names for my various armies, as well, and really enjoyed playing in campaigns (I did a couple with a friend in 40K where it was my Chaos vs. his Marines and then my Imperials vs his Orks in BFG, 40K, and Epic.) I always liked that any decent game of 40K or WHFB could provide a real story in terms of both gameplay and a fictional retelling.
OTOH, there's nothing quite as satisfying as getting a deck to consistently work and winning a tournament, knowing that you're in complete control, knowing each draw as it comes into your hand, and basically watching the deck work like the machine it's supposed to be. You can, of course, also get a ton more games with a CCG than you can a minis game. I don't tell a lot of stories about minis games that I played, but some of those MTG wins still stick in my mind and have been told enough that my friends are seriously tired of them.
In the end, I look at some esoteric factors: I sold all my cards and haven't touched MTG in 15 years. I still have my Skaven, my Sisters of Battle, 3 Epic armies, and two Necromunda gangs. I also still play a close approximation (Battlelore 2nd Ed.) on a regular basis. So, I'd have to say I favor minis and, without question, spent far more money on the hobby than I ever did on Magic (which I also spent a fair amount of coin on.)