I'm glad you asked about down angled fsmash. It was buffed specifically because it did the least damage, and if you notice, the buff amount is actually pretty huge. Now Samus has an extra layer of depth to angling fsmash. Angled up does the most damage, and angled down kills the earliest. Non-angled is a middle ground, though factoring in the extra damage of angled up it probably kills about the same as angled up in most cases. Of course, they have different hit areas so it's not like they're fully replaceable for each other on that basis, but it should be pretty interesting. This angled fsmash stuff on Samus was actually some of the very first stuff done on Bbrawl, as an aside. Of course, testing revealed some implications, and the main one I noticed was that down angled fsmash hits over a similar area to dtilt which makes it basically a slower, stronger, chargeable dtilt that is independent from dtilt in the stale moves queue (staleness being a big concern for Samus if she wants to kill even remotely low). That keeps Samus always having to work for kills while simultaneously making sure she is far more likely to have a usable kill move.
As per the super missiles, I confess to having been completely unaware of that sort of follow up, but given that Samus is a keep-away character, I would imagine super missiles keeping them out better is a bigger deal than getting follow ups off super missiles. Thanks for making us aware of the trade-off there; it's interesting to say the least...
Also, Samus fans should try out the test version Thinkaman threw up a few days ago (though you'll have to compile it). The throw mods for her are... very helpful. Uthrow and dthrow set up for stuff better, and fthrow and bthrow put the enemy further away (bthrow is particularly good on walk-offs, as an aside). IMO they fit into her game quite well.
I should also stress again, just in case anyone is unclear. There isn't some set number of "points" that each character gets, and there's no optimization problem to do in terms of trading buffs. It's just about making the characters balanced; whether that ends up requiring one million changes or zero changes for a particular character is totally immaterial to us. If a change doesn't turn out to have that big of an impact on gameplay in the end, that's not necessarily a sign it has to go (some changes are known to be incredibly niche, such as the Farore's Wind changes). This last paragraph is just something I feel as though I have to repeat every once in a while.