I'd go with the MCSE - if you choose the correct track, you'll be able to pickup the MSCA en-route.
The exams have got harder over the years - I got my NT4 MCSE in 1999 and those were a joke. The Win2k (design) exams were more difficult and the Win2k3 ones slightly harder still.
I found the Cisco CCNA exam more difficult than anything MS offer, but would only advise going that route if you'll be moving into a role dealing with Cisco kit on a day-to-day basis, otherwise it's a bit of a waste and unlike the MS track there is a periodic recertification requirement.