Street-level games have been my favorite since 2nd Edition. I've been running one for about 20 months now and when I do the math I find that a little less than half the PCs have been magicians or adepts (and, of those, more adepts than magicians). If you're playing a "magic is rare / fear it" environment then this might be too many for you, but otherwise I've found that people play by flavor rather than mechanical supremacy. Perhaps your group specializes more or is more combat intensive than ours (which is 75% RP / 25% combat).
Some thoughts based on my experiences:
1) I capped skill levels and provided guidelines for dice pools. This helped and, in fact, gives players the freedom to spread out a little more rather than dumping their finite skill points into one or two specializations. I always recommend this for street-level games.
2) I capped Magic in part to guard against Magicrun. I capped it at 3 for mystic adepts and 4 for everyone else, but if I had to do it all over again I'd knock it down another point, maybe even two depending on how gritty you want to get. Make it so that buying the next Magic point is competitive cost-wise with initiating. Use and enforce the Initiation rules, namely the need for Arcana and the non-running downtime that initiation requires.
3) Be conscious of Edge, how often it refreshes, and how often dice are rolled. In a low-power game, high Edge ratings can really throw your dice pools out of whack, especially if your group RPs more, rolls less, and the players can afford to Edge every roll. (Who needs wired reflexes when a point of Edge will buy five initiative dice? Mr. Lucky can do that all night long.) I had to slow the Edge refresh rate down significantly to adjust for this, which made the use of Edge tactical instead of automatic.
4) If there are still concerns about Magic being too dominant, allow the mundanes to spend their E priority on a second dose of Resources (an extra ¥6,000) instead of getting nothing for Magic E. If mundanes need a LOT of help/encouragement, allow them to take a second priority of Resources at any level.
5) Normally I would be offering advice to make sure the monetary rewards of your missions are keeping pace with the karma awards, since the Awakened benefit disproportionately from karma, but it sounds like you've already adjusted for that. I've been too tight with money in my game because I wanted the players to be scrappy and resourceful, but it just means the magicians have been creeping ahead of the street sams.
My chargen rules are
here if you're interested. I didn't use the Street Scum rules because 1) I didn't see them and 2) I didn't see them. If I had to go back and redo the chargen rules, I'd probably use Street Scum instead of Street Level. Good luck with your game. Let me know how it goes and what works for your group and what doesn't. I'm always tinkering.