Mainly comes down to reputation (which stems from corruption), language barrier, and an unfortunate circle of lack of popularity. Lots of people look at it and think "No one uses Romania, so why should I?"
It's also unfit for growth. If you plan to keep your business small, maybe it's fine if you can overcome the other hurdles. But if you have plans that exceed millions, the tax advantage of Romania quickly dissipates. Same with Latvia. The corporate and tax laws of Cyprus and Malta (and most other jurisdictions) are fundamentally equipped to handle large international businesses, whereas micro-company legislations aren't.