The Nexus 4 really isn't a flagship handset, it's the reference device. If anything you're more likely to have issues as it will always have the latest and greatest firmware - that's the whole point. You just need to accept that being on the bleeding edge doesn't mean great app compatibility always, if you want that then go for a more consumer focused device like a Samsung Galaxy S3.
Actually the Gs 3 seems to have more problems with apps than any other phone especially when it first came out, always read on the "what's new" tab that there is some fix for the GS 3 (read about people having force closes etc.) and certain apps aren't compatible with the GS 3 either, same goes for sense powered devices etc. although it doesn't seem to be as bad. I think the exynos chipset plays a big part in this as apparently it is terrible to work with/develop for as even the CM team are mouthing of about it.
Apps are mainly developed for stock android (pretty much every app developer uses a nexus device and this is their main testing device for the apps as well as maybe a few other phones running different hardware and android skins) and there don't seem to be any problems with the apps on nexus devices, unless you get a brand new android update where the app has to be updated in order to work with the newer version of android.
Your lack of experience with Android is really showing here. Vanilla Android has all the features you could possibly want or need, it's feature rich. Manufacturer versions just rebrand the features with ugly skins and name them stuff like "S-Voice" with touchwiz or sense.
Many people much prefer Google's version which is vanilla Android, it is no less feature complete.
Not quite true, the custom skins have far more features etc. included, whether it be a separate feature or included in the stock apps i.e. all of Samsung smart stay features, HTC's social integration/widgets etc. I find stock android to not have enough features and to pale in comparison when it comes to certain things.
The stock apps of sense/touchwiz will usually have all the features of stock android but more i.e. just compare the camera, calendar, gallery, SMS, mail apps etc.
Plus, some people actually like the custom skins, the only thing I like about stock android is the theme/colour scheme, gets updates faster and that is it, the stock apps are crap (IMO) compared to sense/touchwiz stock apps. I love sense V4 and sense V4+ is looking even better. Touchwiz is nice as well but the colour scheme for it is awful and it doesn't have the same unified feel as sense or stock android, not to mention the apps look very disorganised and poorly "put together".
But surely the S4 Pro + Andreno 320 chipset is bleeding edge at the moment? Is it not supposed to be better than IP5 hardware and more battery efficient?
Yup the CPU/GPU, RAM are the best there is and the screen is supposedly as good as the iphone 5 and one X, if not better.
Although the camera seems to pale in comparison to the one X/S and GS 3/note II as well as the audio.
Can't judge battery yet till people get theirs hand on it.
Still taking everything I hear about the nexus with a huge pinch of salt though till I see some user reviews and gsmarena as well as anandtech's review (with the latest software)