Practice with the long/short or slow/fast method. Somebody else posted a pretty good description of this recently, but I'll repeat it anyway.
1) First note short, second note long. So in a C scale this would be
CD -- EF -- GA -- BC -- DE -- FG -- AB -- [then down] CB -- AG -- FE -- etc. (do 2 or 4 octaves to make it come out even).
The two notes that are together are played really quickly, then you wait before playing the next pair. This isn't just dotted notes, or even double dotting, but a really big contrast between the fast steps and the slow steps.
2) Now do long-short: C -- DE -- FG -- AB -- CD etc.
After you've mastered those two, move on to triplets:
3) CDE -- FGA -- BCD -- EFG -- etc. [This one doesn't come out even unless you do 3 octaves. But actually I like to do 4 octaves and keep going up and down. Then it will come out even after 3 up/down repetitions. The triplets will fall in a different place in each repetition.]
4) Four notes: CDEF -- GABC -- DEFG -- etc. If you want to be really thorough, follow this up with:
CDE -- FGAB -- CDEF
CD -- EFGA -- BCDE
C -- DEFG -- ABCD
The four-note patterns are considerably harder to do correctly. But in all of these, if at any point you feel you're not playing the fast groups quickly enough, the fix is to hold the slow note longer. The idea is that while you're holding the long note, your brain is preparing to play the next short note group. If you do all the combinations, your fingers will get the experience of playing quickly through every combination of notes, including the ones where you turn the thumb under. This method is excellent for improving evenness of tempo and dynamics -- it gets you away from those amateur-sounding scales where the accent always falls on the thumb note.
When you're practicing a scale, start with these patterns, and only then play the scale in the normal way with the metronome. I actually like to play the scales "too fast" at this point, not caring if I make a few mistakes. I have to do something to get my fingers used to playing fast!
This method also works for scale passages you find in your pieces. You can use it for arpeggios too.