I can see having the mobo repaired if by some accident you've busted a port on the rear. The ports themselves only require a decent soldering ability to swap out. You won't be able to change them, the traces to the ports are specific, for instance you can't change or add an hdmi port from a vga port, they are totally different sources.
What remains is a choice. If you consider most mobo's are less than $200, an electronic expert solderer is going to charge a shop fee, parts fee, labor fee etc and the total cost will likely be more than a simple mobo replacement, with new warranty etc. The only time I can see fixing a mobo being viable is if it's a specialized mobo that's semi-impossible to replace, being far cheaper overall to fix.