If you're more interested in the easiest build pathway go IO-390. I have the Thunderbolt version, but if I were building again I'd think a litter harder about going with stock IO-390. I really am happy with the Thunderbolt, but having flown the factory prototype for training with Mike Seager, I'm not sure I can tell a difference. If budget is important, I think the stock engine is great. I did go with one PMAG/one magneto - many options there as well.
Going with the IO-390, in general, smooths the road for a builder: everything in the finishing and firewall forward kits is set up to make this easy. The more "standard" you go in the -14 build, the easier things get. I went with Airflow FM-150 fuel injection which required some minor mods, but the standard system is very good and proven and is easier to install with the Vans supplied kits. I did like working with Don at Airflow to tune my system - Airflow's technology and tech/customer support are superb.
I know builders who've done different fuel systems (fuel return lines etc), fully electronic ignition and fuel injection, and many other changes to the standard setup: these choices are great but no doubt add lots of effort to the build process. Bottom line: how much time do you want to spend adapting your choices versus the smooth and proven pathway of Van's excellent standard kit choices?
Ignition is an interesting question. I recommend you read up on the magneto timing discussions around IO-390, maybe even talk to Lycoming. Angle valve engines have different timing requirements from more common parallel valve engines, which makes the method and programming options of electronic ignition systems an important topic. I went with one PMAG, one magneto mostly because I like the idea of two independent sources of ignition. However with the IO-390 you need to use the less aggressive profile and retard timing a bit, and it's been pointed out to me that in cruise I'm effectively using only one ignition source due the variable timing curve of the PMAG vs standard mag. I may eventually replace the old school magneto with a second PMAG - I suspect this will result in some improved efficiency. If I were building again, I'd go fully electronic with PMAG or another vendor - that would require some added work because (at least at the time I ordered my engine) Lycoming will do no ignition, standard mags, or 1PMAG/1standard mag. I'd have to mount the ignition myself if going with another option: not necessarily difficult but no doubt adding some time/work to the build.
I am happy with stock exhaust: again Van's makes the standard option very easy to go with - Vetterman has a great reputation but from what I've seen, requires some mods to standard setup. IIRC, their system exits the cowling forward of the tunnel that's in place for stock exhaust but don't hold me to that...