Smash's development, like most projects of its production scale, tend to be very waterfall-y. (Post-64) We know Sakurai puts a lot of effort into his project plans, and seems to follow them pretty closely.
Known or suspected deviations from the plan are rare, outside of content cut due to running out of time:
- Possibly aspects of Melee Ganondorf, as his Spaceworld model was retrofitted to Falcon's animation rig very late
- Sonic being re-included in Brawl, after Sega initially said no
- Possibly Diddy's down-B in Brawl, if Dixie was a tag-team character linked to him and used it
- Robin substituted in for Chrom in 4. (Suspected)
- Addition of the clone characters in 4; additional replacement costumes created in the slots for the original characters, and ZSS
- Various aspects of 4 that did not work well on the 3DS, like Balloon Knockback, multiplayer Smash Run, 3D models for Pikmin and Flying Man, and possibly character transformations in general
Across the 4 sequels and their daunting complexity, this is a very short list.
Robin's substitution mid-development in 4 was the biggest alteration we suspect, and we don't really know how early/late that was.