Frankly, it's more about tactics than builds.
1: Solo bosses go down VERY quickly. It's the nature of the system--one Wild Card vs. many, even when the one is considerably more powerful, will almost never actually be able to withstand concentrated assaults (the exception is where things like blanket immunities come into play--and in SR, there's usually some party member who not only can get around that issue, but can make it so the rest of the party can, as well). The lack of Save-or-Die effects in the game has a lot to do with this--you can hinder someone a lot, but taking them out with a single roll for the rest of the combat is pretty much just Puppet.
2: On the flipside, yes, an army of Mooks will tend to go down hard and fast. For these battles, where there's no WCs on the antagonists' side, your best bet is to use the
Quick Combat rules and move on. Let the players describe HOW they are awesome against the mooks, rather than worrying about every step of the combat.
3: The best way to set up a final fight, on the other hand, is multiple Wild Cards (whose abilities synergize at least a bit) and a force of mooks to act as cannon fodder and gang-up helpers. I usually aim for 1 WC enemy for every 2 PCs, then top it off with mooks who make sense. They don't need to be significantly more powerful than the PCs, either--just have them use intelligent tactics, targeting one or two PCs at a time, and they can force the players to go on the defensive.
4: On tactics: Just because one of your villains draws a high card, doesn't mean he should jump into the fray as fast as he can. In particular, if he's got a decent Agility, have him go On Hold. Wait for either the opportunity to Interrupt a PC's action (any effect that causes a PC to become Shaken will make them miss their turn, in addition to any other effects), or to work in sync with a slower ally (if your villains have some way to reliably Shake an opponent, for instance, have the fast combat character go in immediately after that--Shaken targets can be wounded much more easily).
5: Hindrances are a thing for a reason; make sure they come into play. Ideally, every character should have at least one of their Hindrances come up in the course of an adventure, if not an individual session. This should be on top of whatever the 'balanced' fight you've come up with is. Someone has an Enemy? Maybe the Enemy sends out a bounty hunter or assassin--who waits until the party is otherwise engaged to try to take a cheap shot. If they took Bad Eyes and use corrective lenses, have someone make a called shot to the face--if they attacker hits and Shakes the target, the glasses are destroyed, and suddenly one of the PCs gets the nickname Velma. Remember to dole out Bennies when these things do come up--typically, it's not enough to fully make up for the setback (I frequently have to burn two or three bennies in situations where a Hindrance comes up strong), but it gives the players agency, which is a key element of the game design.
6: Speaking of agency, encourage the PLAYERS to describe bad things that happen to them. Over on the PBP Savagerifts.com board, one of the GMs uses the "Epic Failure" rule--if you roll a Critical Failure, in addition to the normal consequences of a Crit Fail (Technical Difficulties, Spell backlash, etc), you can get a Benny for adding on some particular "Frying pan to fire" scenario. It keeps things interesting, and adds those moments everyone remembers to bring up when it's time for gaming stories.