However, our draft is so thin with 24 teams and prospect keepers that having those 48-72 players available for our draft would do wonders.
Counterpoint: Our FA draft may be a little thinner at the top, but in general it is much deeper than other 24-team leagues I am in because so many uncarded players (prospects that haven't hit the majors, mostly) take up 20-man roster spots instead of player cards in the $1MM to 2.5MM range. And we play with the Unleashed set.
I wouldn't be opposed to eliminating the Supplemental Draft, but maybe with some tweaks, it could remain. The Supplemental gives weaker teams a chance to speculate for the following year, while it gives contenders a chance to rearrange the end of their benches. If you choose not to participate (as several have) and miss out on an opportunity to improve your team, then that's on you.
I'd recommend reducing the number of rounds from 3 to 2. And make only carded players available in the Supplemental Draft instead of any player that was eligible for the FA draft.