Honestly, I wouldn't use Shadowrun as a universal system. It works great in a fantasy cyberpunk game, where you not only have elves and dragons and magic, but also cyberware and the Matrix and deckers, but the internal balance breaks down when you remove parts of it. So outside of a narrow niche, there are simply better choices out there for universal systems, especially since those systems were DESIGNED to be universal.
Two main contenders I point people to when talking about universal systems are Mutants & Masterminds 2nd edition and Champions/HERO System. Both are points-based, effects-based systems, which allows for a lot of freedom in designing characters. If you are looking for a way to do magic that involves having to rest and recover your stamina, then there are ways to do that in both systems. With M&M, you could simply tack on the Side-Effect flaw to your spells, with a 'Stun' power as the side-effect. At the second level of the flaw, every time you use the spell, you'd have to resist a Stun effect. Makes it so you can't go spamming attacks all day long, while not being TOO harsh on a player. As far as HERO is concerned, however, things are even easier. Almost all powers or effects cost Endurance (END) to use. You recover END both at the end of a combat turn and if you rest for one of your initiative passes. So I can spam a manabolt only so long as I have END to use on it.
Another point towards HERO is that they have different kinds of defenses. The four main kinds people worry about are PD, rPD, ED, and rED. PD and ED stand for Physical Defense and Energy Defense, respectfully. If someone shoots you with a shotgun, that will go against PD. If they hit you with an energy blast, that's ED. The 'r' stands for Resistant. That's kindof like Hardened Armor in Shadowrun. There are two types of damaging attacks in HERO, normal and Killing. Normal attacks are affected by your full defense, and while they may knock down your STUN, they don't often damage your BODY. Killing attacks bypass all but your resistant defenses, deal damage direct to your BODY, and also have a multiplier that applies damage to your STUN. Basically, a Manabolt would be a Killing attack, while a Stunbolt would be a normal attack.
The downside of HERO is that it is, if anything, more complex than Shadowrun is, so it takes some work to get used to the system and figure out how to do things. M&M, on the other hand, is based (loosely) on the D20 system, which means that 80-90% of the potential players out there already know the majority of the mechanics, post-Chargen. This makes it easier to learn, though there is a distinct difference in style of play. HERO is a tactical game, whereas M&M has a freewheeling style like you're watching Spidey and Green Goblin battling it out over Manhattan. For a grittier, more 'street' game, I'd go with HERO, but for a high-flying, anything goes game, M&M is a better choice.
