If you expect an informed reply, forum will need complete model numbers of the equipment from each quote...

Option 1:
York 3 TON Furnace YCJF36541S1 and AC TM9X080B12MP
95% efficiency Furnace (2-stage) and 16 SEER AC (one-stage): $6500.00
York Electronic Air Filter SIEAC14001625: $1000.00
Includes upsizing to 8" dull duct in family room at no charge and a 10 warranty on parts can labor.
Includes permit and removal of old equipment.

Total: $7500.00

If I want to add another return in my family room or if possible to upsize current return, the charge is an additional $500.00

Option 2:
(no model numbers)
Rheem Super-Efficiency 16.00 Seer 2-stage AC and 95% 2-stage furnace. $5343.00
Add-ons:
Electronic Air Filter: $1500.00
Upsize one vent: $600.00
Ten year warranty on parts and labor: $600.00
Permit: $100.00

Total: $8143