The apps are considered bloatware not necessarily because of quality but because you're taking a base (stock Android in this case), reskinning and adding extra apps and features that were not present before (or in some cases were but were replaced by an equivalent functioning one) and pushing it out. Anything that adds extra anything can be considered bloat. Is it bad? That's an entirely different story. Alot of stock enthusiasts will try to convince people that bloatware is bad, but who are they to say what someone will and will not like? I personally love the stock Android experience, having used Touchwiz, motoblur, sense, etc. I find the extra features tedious and not necessarily what I need. However my mother-in-law and wife are very different, many of the bloatware apps they use are handy for them. Bloatware just is what it is, it isn't good or bad. As for google's closed source apps being considered "good", again, think it really boils down to personal preference.
That Ars Technica article was interesting, but felt a bit skewered. Google is definitely making some closed-source moves, but that's what you do with a successful product, you start to lock it down before someone takes it from you. Amazon has found some good success with their forked version of Android, Samsung tried and failed with Bada, so it looks like despite closing some parts of the source Android at its core will still live on as open source for people and companies to make use of. Now that aside, Google definitely has some benevolent things it has done, but like anyone else, they're in it ultimately for the money. Like iOS users, as you get ingrained into a particular ecosystem, it makes sense to adopt more of it as it makes your life easier. You apparently enjoy the Samsung ecosystem, that works for you. Personally I am all about Google and all their products, that's just me. My brother loves iOS and is all about that, it all makes sense to embrace the ecosystem you're comfortable with.
To address the Op's question though, I think you should flash an AOSP ROM on one of your devices and see what you think, the only way you'll know if you like it is to try it out yourself. Anyway, that's just my .02 cents.