I agree on that count.

However, some airports seem to have their 'policy' (not sure about their official policy but based on consistent observation) of consistently bringing everyone with wheelchair assistance to the CE check-in queue, and that can actually have quite a bit of an effect on the queue if there are many people being brought to the front of the CE line when there is only one CE check-in desk.

In fact, often there are people in any queue who are less likely to be able to wait in the queue comfortably than someone in a wheelchair such as those who are frail etc., so the situation really needs to be looked a bit more holistically than a simple matter of "Cut some slack for those who are unfortunate enough to need a wheelchair" etc. As far as I can see, no-one is begrudging their right to be brought to the front of a line, but merely questioning the procedure of using the CE queue in particular in the OP's case.

As with what I have seen at certain airports, since it's unlikely that everyone in a wheelchair is in CE or have status, it seems a little strange to concentrate it on a single CE check-in desk when there are multiple lines to choose from.

While I may sound rather unsympathetic, I can assure you I'm not. I was told to expected to have been in a wheelchair by now, and I do face that prospect in not too distant a future even though I am still fully mobile. However, even from that point of view I do not think it would be procedurally right to consistently pick a single line rather than spreading the effects, particularly when the line consistently affected is a premium one, unless there is a good reason to do so such as the affected passenger in premium cabin or status, or using the premium check-in brings practical benefit to the assistance system or the passenger..