Fion:Shadowrun is based on D20 rules (like 3.5e D&D) so yea completely convoluted and overcomplicated :p
SMILE:Magic is the biggest problem, I think, with the whole "cybernetics destroys a person's ability to cast magic" schtick. I'd sugges that "cybernetics" should be treated as a separate "mage" path than the rest. Have cybernetics be rated from 1-5 as a measure of how invasive they are. Then, for each dot in, eg, a Cybernetics merit, you can purchase the equivalent level of cybernetics equipment. (So a three-dot cybernetics merit lets you purchase all cybernetics up to level three.) If a character ever purchases equipment that exceeds their Cybernetics rating in dots, he loses his magical abilities. Furthermore, for each dot of the cybernetics merit that the character purchases, his possible (or actual) power stat for Mages (what is it again- Gnosis?) is reduced by 2.