You already have a great system.
An A3000 will only give you headaches (The PSU is not much powerfull, scsi controller sucks, zip memory sucks, you'll need an accelerator and graphic card, ECS in hi-res is slow if you use more than 4colours, it won't run AGA games/demos and it won't run more games/demos than A1200 -simply use WHDLoad)
I had various machines (2 A500, A1200/040, 2 A3000,2 A4000, A4000T). The A3000 is nice but since I love demos there's no way it could replace my AGA machines.
I have a PPC A3000 with a lot of extras, but believe me: your current A1200 will be better than your A3000 even if you expand it with a 060 card. Since you already own a Mediator I guess you are using a Vooodoo3 right?
Do you really need various machines?
BTW... about your 060 card... have you installed the 68040/68060 libraries correctly? Have you tried Oxypatcher/Cyberpatcher? Have you tried changing the ram type? Have you tried to install a heatsink and fan? Have you tried cleaning the contacts between of the A1200 board, Mediator connector and turbocard? Have you tried to use other PSU? Your 060 card should be stable. Have you tried your 060 card without fast-ata and without mediator?
FastATA sucks... you'd better use the blizzard scsi controller with Yamaha SCSI-IDE adapters.
If I were you I would keep the A3000 as retro-system and expand the A1200 (with a scsi controller for the 060 or a PPC board)