I then watched a few High-ELO Syndra games after I got to grips with the kit, which really propelled me into the I-need-to-be-god-with-this-champ feeling that I'm certain we've all felt before (Looking at you, Forte).
same
wait a second
In regards to the bugs you mention, you may be talking about the Stutter Step Bug (where her ultimate desyncs her model from the game world). This can make it appear as if your whole game is being impacted, particularly if you play with locked screen. Otherwise, there are a lot of FPS drops occurring on recent patches (6.xx series), so that's a distinct issue as well.
As far as fluidity is concerned, 'yes and no', comes to mind. What frustrations I experience are either direct results of other bugs, or design limitations of how the game engine works. I would say, objectively, her clunkiest ability would be W and how its executions tend to work. I can see ping and general latency causing a lot of end user frustration, though, since she is very timing sensitive.
Her early wave clear (pre-first item buy, or pre-80 AP) is wretched, yes. There are some tricks to do at level 1 Q that can actually make it very passable to farm under tower, but that's kind of the exception. At the end of the day, she has to invest a lot more mana and cooldowns (especially if her stun is being used) to do what people like Zed do for free.
This diminishes later as she gets AP and levels, but if you're committing her stun to wave clear, that might be a big problem in and of itself from a design stand point ...
45%, flat penetration, %magic from Ferocity; all viable for different reasons and goals. In general, achieving 45% CDR on Syndra without wasted stats 'somewhere' is a great difficulty. I managed to sidegrade into the route nicely since I utilize WotA, but most others do not like that aspect. Sadly, AP itemization is not efficient (in a very you lose hard outright going this route) kind of way. Ionian boots removes the damage from Sorcerer's shoes, resulting in a net negative DPS loss (even when you're at 45%, the route that's supposed to win in DPS).
I suspect 45% will become a stronger build choice than penetration when CDR itemization is improved. For someone as DPS/tempo centric as Syndra, extra kill power from penetration is 'nice', but faster abilities improves her capability tremendously. The key problem is that doing so is less efficient, again, because of terrible itemization. A bit of a sleeping giant situation, really.
Over all, I can agree with your position of her being 'clunky and weak', mostly on the latter than the former. At the end of the day, a Syndra player has to invest three times the effort of someone playing anyone else (namely Assassins and Mages) to achieve even half their results. Her investment curve is massively skewed to her potential reward vector, resulting in the frustration you mention: you can play someone else who is easier and do much better.
Sadly, I'm not sure how Riot could address this without having her gleefully step on everyone else in the process. She has a unique combination of strengths that can easily and rapidly become overbearing to almost anyone else once they're going. Her once powerful lane bullying pattern, for instance, was one of these and the first thing they were certain to be rid of.
I would like for the day to be for her, one day, that Syndra's real power is in her constant projection around herself. She's not fast, there's no special mobile tricks, but the longer you're engaged with her, the worse it will be for anyone involved. People have to be afraid of being around her, more than her just ... stacking Q + E + R, walk away afterward (Snipe and run strategy).
Who knows.