Everyone has problems with 291. They just buckle down and do it anyway.
While a lot of companies are moving to 2008, Windows 2003 is going to be supported until 2018 or some such. The odds are pretty good that you'll still run across it somewhere, if not still be using it in some capacity years from now. I work for a company right now that still has a couple dozen NT 4.0 servers and at least one NT 3.51 server. On the other hand, I've had my MCITP Enterprise Admin for 10 months now and haven't touched 2008 at work outside of a dev/test environment. Go figure.
But most importantly, in order to get your MCITP Enterprise Admin certification from scratch you will have to pass 5 tests. If you were to complete your MCSA that would be two tests, plus four more to upgrade to MCITP Enterprise Admin. So it's 5 tests to get one cert of 6 tests to get two. I say go for two. The more certs the better (if you couldn't tell by my tag line). Besides, nobody likes a quitter. What happens when you have problems with one of the 2008 exams?
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CompTIA A+, Network+, Server+, Security+
MCTS:Hyper-V
MCTS:System Center Virtual Machine Manager
MCSE:Security 2003
MCITP:Enterprise Administrator