I think smoking a joint is probably the overall best way to consume cannabis, I can say for me personally that it is the method I enjoy the most overall. That said, I still smoke more cannabis through bongs than I do through joints, I smoke my bong every single day, and while I do roll a joint probably 80-90% of days it will make up 30-40% of my daily smoke and the rest will be via my bong. As someone who smokes a couple grams of weed per day and doesn't have a particularly high income it is hard to justify the cost of smoking joints exlusively, because at this stage that would mean spending less of my day stoned or spending more money on it, the latter of which isn't really an option for me and the former isn't too attractive of a proposition, especially while I am currently trying to reduce my daily alcohol intake.
I think the OP touched on a number of good reasons about why bongs aren't necessarily cleaner than joints, and infact, often are the opposite. I also find that when smoking a bong the water filtration just gives it a slightly weird taste, I don't hate it but it is not as nice as the taste of a spliff. I also think that despite many people claiming water filtration has a positive impact on your lungs that it is the opposite, I think overall you inhale more smoke at once more deeply and it is considerably worse for the lungs. I also think unless you are replacing the bong water every couple of uses most of the carcinogenic filtering benefit of water is negated and furthermore, there is potential for one to inhale some amount of water vapours when breathing in hot smoke that has passed through water to cool down. I know when I gave up bongs to smoke joints exclusively for around 6 months my lungs felt much better for it, and I did not once cough up the grey/black phlegm that can be a regular occurence when smoking bongs particularly heavily.
I think a lot of the issue is lazyness and lack of skills, followed up by perhaps a lack of understanding on what are the better papers to use and why. A lot of people never bother to learn the art of rolling a joint, and it does take time to master, they roll a few and smoke their shitty abominations, unsurprisingly finding these canoeing, ugly, harsh, filterless pieces of shit that are likely rolled in a thick crappy paper, to be unpleasant to smoke and rather wasteful. The problem is they don't judge how efficient a joint is based on a joint that is actually rolled well. I honestly find that I have to use probably 1.5 times the amount of bud in a joint as I would in a bong, the stone wont be quite so pronounced but it also has a slower come on where I get to appreciate the whole spectrum of effects as I slowly descend into stonedness and it also lasts about as much longer as more weed I am using (1.5 times or there abouts). I also find that smoking joints doesn't really lead to a shitty burnt out feeling when the high wears off, which bongs often do, as a result of this I can often smoke a joint and get high for an hour or two through the day without having to resort to smoking all day to not feel shit, something that usually happens if I smoke bongs in the morning or through the day. As a result of this it can technically save me weed to skin one up during the day as opposed to hitting the bong.
Joints also taste better (if you use shitty papers then maybe not, but good papers aren't that hard to come by), are more social and also just the process of skinning up is a great ritual and for me leads to enhanced enjoyment of smoking when I construct it with my own two hands. I find that smoking bongs are rather clinical and focused where smoking a joint is much more relaxed.
Sadly, in the country I live there is a really anti joint mindset amongst a majority of cannabis smokers, they would rather fashion dirty bongs out of tinfoil, plastic bottles and garden hoses than learn how to twist up a work of art. I understand this mentality completely if you are 14 years old, spending your weekly allowance on a gram and ditching school to go get high with 4 other people, but what is crazy to me is I know many working adults who earn good money that are repulsed by the idea of rolling a joint, citing it as wasteful. While I do appreciate that at times one has to conserve their stash, if the point of consuming cannabis is for personal enjoyment then I don't really see why one would sacrifice a better experience just to save weed each and every time. Sometimes the way to get the most out of something isn't to make it last as long as possible, but to enjoy it as much as possible. Most of my friends look at me like I am crazy when I am round at their house and they have a mix going and I pull out a bud and my pack of OCB's, shit some of them even refuse to take a hit off a joint I fucking rolled which I don't get at all. It really makes me sad that the art of the joint is largely unappreciated where I live and I honestly can't figure out why the mentality is so different in Europe.
Don't get me wrong, not hating on bongs and it is very much different strokes for different folks, but I do think that in recent years joints are being increasingly overlooked by cannabis smokers in favour of fancy glass gadgets and that is a fucking shame.