Pathfinder addressed the issue of Monk's BAB in an elegant fashion (IMO).
A Monk keeps her medium progression BAB (3/4 level) but, when she uses Flurry of Blows, she applies her entire class level as BAB albeit a penalty for using the equivalent of Two-Weapon Fighting.
So, at 1st level, she has BAB pf +0. But if she takes a full-round action to flurry, she can make two attacks at -1/-1 (+1 for the Monk level, -2 for the two-weapon penalty).
Penalties never reduce with level, but additional attacks are gained as per Two-Weapon Fighting feat tree. In detail:
Level 5: BAB +3, Flurry: +3/+3 (+5 -2 plus additional attack)
Level 6: BAB +4, Flurry: +4/+4/-1 (+6/+1 -2 plus additional attack)
Level 8: BAB +6/+1, Flurry: +6/+6/+1/+1 (+8/+3 -2 plus two additional attacks)
Level 11: BAB +8/+3, Flurry: +9/+9/+4/+4/-1 (+11/+6/+1 -2 plus two additional attacks)
Level 15: BAB +11/+6/+1, Flurry: +13/+13/+8/+8/+3/+3 (+15/+10/+5 -2 plus three additional attacks)
Level 16: BAB +12/+7/+2, Flurry: +14/+14/+9/+9/+4/+4/–1 (+16/+11/+6/+1 -2 plus three additional attacks)
Level 20: BAB +15/+10/+5, Flurry: +18/+18/+13/+13/+8/+8/+3 (+20/+15/+10/+5 -2 plus three additional attacks)
I think you could apply this rule as is, substituting the whole 3.5 Flurry of Blows mechanic.