"When i upgraded to a 3 ton 2 stage from a single stage 3 ton HP, i have noticed that except on mild days, it would take forever for first stage to satisfy the thermostat."
Which is exactly how it is supposed to work.
"I should have had them move up to a 3.5 ton unit"
No, you shouldn't have.
"so that first stage would work better and then on temp extreme days 2nd stage would work more efficiently and not run as long."
Running non-stop gives you the best possible efficiency, cycling reduces it, so it wouldn't "work better".
"I will have to make sure to do that for my next unit!"
Your funeral.
Design conditions means the temperature that is exceeded just 1% of the time on a 30 year average.
For me for cooling that's 90° F outside. Designing for 75° inside means a 15° difference. I personally prefer closer to 70°, but we'll go with 75°, it makes the math easier. A 2 stage has say a 66% capacity in first stage so a 10° difference.
So theoretically assuming no other fixed heat loads in the house and no solar gain, IE just an empty shaded box with an A/C that's exactly the right size:
75° or lower outside, system never runs.
76-84°, system cycles between off and first stage.
85°, system runs non stop in first stage
86-89°, system dithers between first and second stage
90°, system runs non-stop in second stage
91° and up, system can't maintain set point. This is the <1% of the time conditions.
With the solar gain and interior heat loads the system will start to run when it is cooler outside than inside, and of course system capacity decreases with increasing outside temp and hence head pressure but it just skews the span of the numbers, not the conclusion.
Intentionally oversizing so that you are covered that <1% of the time will cost you comfort and efficiency the other 99% of the time, which seems foolish to me.