I went and did frame counts.
Syntax:
Level name: Time change (in frames) in levels, time change in boss fights.
Positive numbers benefit fractalfusion, negative numbers benefit parrot14green
Reploid Factory: -51, -62
Wire Sponge: -81, +3
Wheel gator: -136, 0
Flame Stag: -43, -4
Bubble Crab: -41, -1
Magna Centipede: -5, +17
Crystal Snail: -107, -1
Overdrive Ostrich: -94, -1
Morph Moth: -99, +2
Sub-Total: -704 (11.733 seconds)
Sigma 1 (Violen): -26, -13
Sigma 2 (Serges): -40, -100 (?)
Sigma 3 (Shouryuken, Agile): -100, (Skipped)
Sigma 4 (Rematches, all at once): +13
Sigma 5 (Level): +50
Zero rematch: -32
Neo Sigma: +44
Wireframe Sigma: +1 (?)
Sub-Total: -173 (2.883 seconds)
Total: -877 (14.616 seconds)
Disclaimer and notes: I am not infallible, I may have made some mistakes but overall I think they're correct to within 1 frame. Numbers marked with (?) may be subject to a higher degree of error. I skipped measuring Agile getting punched due to difficulty measuring the start point, and I should hope the equal. Some non-playable but time-affecting numbers (such as Flame Stag's supposed death delay if he's in the air when he dies, post-death lag, stage select speed, etc) are not noted. This post is intended to try to separate superior playing from a ROM change.