Honestly all systems have their good/bad points.
Master Seal system is overall the best.
"Promote at 21" worked well in Tellius, even if in lategame overseas RD they undermined Master Crowns (and Holy Crown in particular).
Gaiden/SoV system is good, but the variation used in Genealogy punishes mid-chapter promotion hard (unless it's in chapters where you might need to backtrack close to your home castle, considering the size of the maps.
GBA system is IMO the worst, as it's sometimes needlessly restricting. Examples include mages/clerics in FE1/Mystery book 1 (you don't get guiding rings at all until chapter 19, at which point you're on home stretch towards endgame, what the hell), Rutger (who undermines every other Hero Crest user for a long time, simply because they don't get to promote until chapter 12 IIRC, and even then you only get to use one such unit, the third crest comes a bit late), Pirate Ross and Colm (they undermine each other since you don't get another Ocean Seal until chapter 14 secret shop) and, to an exent Matthew and Legault (Fell Contract comes late, and if you want to promote both, you have to buy another one for a massive 50k gold).
Three Houses system is very unusual, and is a bit rough around the edges. I'd say get rid of RNG chance to pass, but in return, lower the reqs. Byleth in particular needs the RNG on their side to get into advanced classes the moment s/he hits 20.