First please ignore my username as I am not a handy-man but an hvac tech.

If you keep losing refrigerant, that means you have a leak somewhere, which is a major problem depending on where the leak(s) is/are.

1) would you agree with the assessment I should replace because of its age? Service guys point was that the compressor useful life is only around 15 years and doesn't make sense to put money into it and that I can expect to have furnace problems.

Yes! absolutely especially when you have refrigerant leak.

2) do I have the right size units, 3 & 2 ton. I don't know the furnace specs? Service guys response was that the engineers who decided this 20 years ago knew what hey were doing. My 2 story house is 3,000 sf plus 1,000 sf finished lower level that may not have been in the calculation when the house was built.

Since your house was modified, a heat/load calculation must be done in order to know.

3) is there a reason to stay with carrier just because the other unit is carrier?

Not really, carrier is a good brand, but you can choose different brand. Most of the units now a day are equally good. Just make sure you choose a good contractor to put it in. Good contractor will determine the longevity/efficient of the unit.

4) what efficiency/spec levels should I be considering?
Depending on your electric bill. If it's high, go with most efficience unit, if low just stick with the bare mininum. Always make sure you ask for warranty!!!! Ask for labor and part warranty, and make sure you have it in writting!

good luck on choosing a new system.

Thank you for the helpful comments. Is the heat/load calulation something any good HVAC guy should be able to do?