So I hit VA but couldn't see the quantum slipstream skill anywhere. Someone told me I had to spend all my skill points, but I ended up having 500 skill points left over that I can't spend on anything -- the cheapest skill I have is 1000 points...has this ever happened to anyone else?

I recommend lowering one Tier-1 skill by one level, which would give you 1,000 XP. Then spend your points on increasing a Tier-2 skill by one level, which will cost you 1,500 XP. This would spend your remaining 500 XP plus the 1,000 XP you got from lowering your Tier-1 skill by one level.

This should basically be a bug but they call it a feature.
Because it´s easier to make the player waste a respec token than do something arcane like have the game check if your last two skill-tiers will leave you hanging with those 500 points.

I have the 500 points left over too, though I found the slipstream power in my pool (hit p) and could drag it to the tray.
And I think missions also give me the highest loot now, not sure. Have to check with the paratrinic shield mission when I find the time.