Although I agree that flagella probably need revisiting, I think the problem here is ill-posed. Your example species are of respective size 3, and 32-53, which means an average body volume ratio of roughly 11-18. That is a lot. Being large comes at a high cost, since you have to find more food. This is why most species are small, and even microbial. Large species of course exist, and so it is key to understand why they came to be.
Some thoughts on it
Being large yields two benefits : better osmoregulation and greater “strength”. The former being not implemented, let’s just focus on the latter: what I called “strength”. It roughly translates as: the bigger, the easier it is to win against another individual. This is interesting for both predators (who can hunt more easily) and preys (who are less at risk to be eaten).
These opposed pros and cons for size (less food/faster vs. better regulation/stronger) are very interestingly represented when comparing the mainland to islands. As there are little predators on islands, species there tend to develop either gigantism (for regulation) or dwarfism (for food). For those interested, an insular human species probably developped nanism: Homo floresiensis, in modern-day Indonesia.
So, like insular species, an isolated species of our microbiote would end up developping dwarfism (and not gigantism since we have no osmoregulation interest in being large). What this tells us is that as of now, there is a definitive pressure to be small.
For a predator, who simply needs to be larger than their prey, this means that it will be optimal to be only slightly larger than their prey, favoring small body-size ratios (currently 1.5). This means that large species can only occur, as of now, through concurrent evolution, with a prey cell growing large and a predatory cell growing even larger.
As such, I’d argue there are 3 ways of dealing with this issue of size:
- go with concurrent evolution, which is almost implemented (although there’s no penalty for being a prey as of now I think?);
- add osmoregulation bonuses for big bois, although that will probably be dedicated to fairly sessile, non-predatory organisms;
- dig a bit more, since there are microbial species with a 50:1 body-size ratio for predation; however this does not take into account the fact that they may have other propulsion methods (esp., at least some are ciliate) and that these small preys may not be the bulk of their actual predatory regime.
By the way, we should also probably note that, although there are some cases of predators smaller than preys, this remains an exception: it only is about 10% in animal communities. Of course, we’re dealing with microbes, so that may not hold perfectly, but still.
There’s much more to say here, but I believe we should focus on this question : how much do we want these big cells to be good predators for these tiny cells? I for one am fine that this big species does not predate much on the tinier. I feel we should rather focus on species of size 5-10 for this purpose, and try to get bigger cells evolving for richer predation.
For the matter at hand though, I’d also like to point out that flagella normally lose efficiency the further away from the central axis (which we might want to reconsider), so your build is not optimal. And I agree this would make auto-evo more in favor of this (although, perhaps not before we’ve fixed the final balance bug).
All that being said, I’m in favor of 3.
As a final note, an article (under a paywall, alas), that could be of interest : Effects of Predator-prey Body Size Ratios on the Stability of Food Chains - PubMed