We have both --- guess it depends on one thing --- how much you want to learn.
Our baja is a stock 2.0 FI --- it came complete from a running bus... it does take some extra wires to the front and an extra return fuel line.
Unless you're good at reading and electronic testing, many times the FI system you're buying on ebay was removed because it has a running issue.
Biggest drawbacks of FI... time... research... testing... and routing electrical/plumbing to the front.
I love it --- but then again I'm a freak.
T.