Same experience with the 1" thick 16x25 $10 and $15 filters from Home Depot hurting the flow.
In fact, did some testing and found it was so restrictive that lots of air made it past the filter's edges because it was causing that much of a restriction. It was mounted like junk too, but even with some new brackets it would flex and leak, very frustrating.
Instead, went on ebay and found an AprilAire electrostatic 5" thick paper filter. It was only $400 at the time, and that is so much cheaper than paying a shop markup+labor it seemed worth it to try it. Price has since went up, and you're not supposed to be able to buy them alone and put them in yourself. In fact, if you're not up to electrical code and wiring and the sheetmetal (or fiberboard) work you maybe shouldn't try to put it in.
It was an incredible amount of work to put in, not so much rigging up a sheet metal brake and making the connecting metal box to space up the unit so I could slide it out and clear my gas line that was haphazardly ran, but just building a 2x4 platform in the confines of the attic trusses and braces with an extra foot of insulation blown in was a nightmare. Had it been like a house in the northern lattitudes where the furnace would be in the basement it would have been 1/10 the work without the confined area.
Anyways, to the point, after installation the difference was very impressive. It was like the blower was on low before, you'd have to put your hand in front of the regsiters to see if it was blowing air. Now you could just walk by them and you could feel it on your face and arms! Seemed to cool a lot better, no hard data or measurements but it seemed to make the system much more efficient. My neighbor does home remolding, he took a step back when I turned the system on and he felt the air coming from the register in the dining room, so he was very impressed too.
Try taking out the filters completely and see if there is a difference in flow that you can feel. If so, in the future you might want to try to install a holder for a 4" thick filter from Home Depot, you get a lot more surface area from the same sized opening. This means less restriction and will get close to the flow rate without a filter.
It might be all in my head, but with putting in a new filter in my unit just recently I feel much less of the pollen effects here in Atlanta now then I did before replacing the filter (recommended every 12 months but it was so dirty I think I'm going to do 6 months).
Maybe one of the HVAC engineers who post here regularly could post data on how much those filters affect the units performance instead of just anecdotes.
For now, you might just want to experiment with one filter and see which works best. Fancy filter to knock out pollen, cheapie filter if it flows better and takes out enough pollen to be liveable.
