I'm confused by the discussion so far: Stroke and rod length are pretty much independent of each other.
Rod:stroke ratio is an important consideration.
Assuming everything else remains constant:
The longer the rod, the lower the side-loading on the piston/bore, the lower the peak acceleration of the piston, and the greater the dwell time of the piston near TDC.
The downside is that it makes the motor taller/wider, and increases the peak piston speed. There is a theory that says a too-long rod can make engines with 4"+ bore more prone to detonation, but that doesn't seem to hold much sway with modern fuels and ignitions.
Broadly speaking, a performance 4T motor will benefit from a larger bore and smaller stroke (for any given cylinder capacity). The larger bore gives more room for valves and the shorter stroke reduces the loads at any given engine speed.
You can see this with any modern 4T bike motor.
Also broadly speaking, 2T performance motors benefit from longer strokes and smaller bores. You can see the way this has evolved in all of the 2T MX motors - they've all moved toward longer strokes over the years - even the YZ & KTM85s are undersquare nowdays.
The 144/150s with the 58x54 dimensions are the exception, but that's largely because they're an adaptation of a 54x54 125 motor - TM and KTM have both made dedicated 144 motors that are undersquare.