I've done both and think I prefer same day. I'm doing same day currently with a variation of PHAT that has two days strength (upper/lower) and three days hypertrophy (push/legs/pull).
When I go really intense with squats and deads on different days, it kills my CNS. If I alternate heavy and light to not burn out, I feel like I'm missing out since they are both best performed heavy. Doing them same day gets about 85% of the weight as separate days but doesn't wear me down!