I see a lot of 4 cylinder cars whose bore is around that (84-88); long time ago you could find 2.3-2.5 engines with 96mm bores so they were more on the oversquared side. Is that now considered bad nowadays?

 

Maybe they went with a smaller bore for the advantage of lighter pistons I don’t know. With a bigger bore you can fit bigger valves though

 

Not sure how new of engines you're taking about, but the new stuff that's been coming out is almost pushing towards diesel-like. I think they're increasing compression and stroke in order to raise efficiency and torque. Which I'm a fan of anyways, I moved away from gas along time ago because I hated that in order to speed up or pass someone required you to floor it and downshift. Where as with diesel the turbo and torque would let you just go.

 

Efficiency does not equal power
New engines with modern design strategy may be more efficient than old design,
but old designs are simple and work well maybe without the efficient use of fuel.

For example Toyota 2jz and Nissan sr20det, 1995-2002 models
both 86x86mm borexstroke design, almost identical
2jz support 700-800rwhp for 25 years at 3.0L displacement Iron Block
sr20 supports 450-500rwhp for 25 years at 2.0L displacement Alum Block

8.5:1 compression, turbo friendly design, oil squirts, girdle support, seq EFI, cast alum piston.
2jz will 25-28mpg @ 3200lbs
sr20 will 28-32mpg @ 2800lbs

Very simple design, minimal electronics and emissions, these engines are the pinnacle of performance vs complexity. It only gets worse from there. Modern engines of similar displacement might occasionally support a hair more economy and power, but the difference in complexity isn't worth the extra couple percentage of efficiency if you are the one working on them and tuning them, maintaining them, replacing them.