They are both great bikes.
The build quality on the Cagiva Mito is amazing, but parts can be tricky to track down. Regular maintenance isn't an issue and there are top end parts still available. Cagiva Mito is a timeless design, original design before the 916, and is the rarer of the two. This is a bike that can be a showpiece or cafe runner.
The Spains No. 1 era RS125's are decidedly more modern in design and uses less special hardware, fasteners, mounts, etc. when comparing to the Mito. Parts are readily available still from Aprilia dealers making them easy to own. I would say the Aprilia is the better handling bike and better for regular riding. Being the most modern 125 available, it is the most refined to ride.
Comes down to if you want something really special or something you plan to ride more regularly.
Jenius Biker Blog
Current FTR, Metro, RS250³, V7, RC39, TT
, Bangkok, 85 ADV
Past: Newd, Zuma, Diavel, Zero, Grom, M696, GTS300, KLR650,SC1000s, CeRbi, SPR, 959 Corse, CB300R, SRMotard, Versys, Typhoon, NCXD, RC390², Madass, PW50, KTM BR 65, Aprilia BR50, Aprilia RS125², DRD, WR250X, Derbi SM⁷, Aprilia RS50¹⁰, Derbi GPR³, Aprilia RS250², Mito², NSR50², NS50, HRC RS125, HRC RS80, YSR63 (1st 2stroke!), FZ600, KLR250(1st Bike!)