I suppose it's down to personal choice, I'd MTDI an AFN, because it's much more simple and easier to install, in a transplant situation, there's much less wiring for the installation, and much less to go wrong afterwards. If you're happy with the extra complication of the electronic systems, complete with a barrow load of wiring, then go for it, I'd wager it'd be more reliable than if you were to fit a Mk 6/7 engine.
I'd bet I'm one of the cheapest members on the forum, (ask Tim
) I don't give a toss about bells and whistles, I want to spend as little as possible, and still get reliable motoring with reasonable performance/economy, without getting any nasty, expensive surprises. Old VAG cars, with the 1.9 TDI, Audi 80, VW Passat, have served me well over the last 10+ years, 20,000 miles per year, no breakdowns due to engine management, or mechanical problems, with fantastic performance and economy, for what they are ( they don't seem prone to rust either ) with just regular servicing and the odd ball joint etc. I see little prospect of me MTDIing them or changing brands in the near future.