you really should arrive in the present not to mention the future … but thats another thread 
I hated that you could see runways >30 miles out…they stood out way too much. This is still a slight problem in MSFS.
1.)
In the FSX era was no YouTube to teach me navigation and flying! This was what I hated most, no one and nothing out there really teaching me how to fly by the book, the procedures, VOR and ILS and other things.
2.)
And of course the FSX graphics meeeh…
I had some truly great airplanes with beautyful virtual cockpit, even Captain Sim was good back in these days - but the visuals outside of the cockpit window were rather bad. (Even with REX Clouds and terrain addons and whatnot… I had 200 GB or so upgrades and addons installed which was tremendous back then!).
Blurry, generic, no interesting nature or terrain or mountain details, nothing to see in a boring generic world made of generic texture tiles, no dense forests no beautyful beaches or coral reefs visible from above when flying over tropical sea areas.
OrbX was the first update that really enhanced the FSX visuals, instead of making the vanilla graphics looking exactly the same but only some roads and houses placed different.
I really started to love FSX when OrbX, REX PMDG and Carenado appeared.
3.)
Not ecactly an FSX problem but computer hardware was rather slow and expensive during the FSX era - no matter how much money I invested in hardware I still had 15 FPS.
No superior Ryzen power out there to save us all! 
But when thinking back I cannot remember anything particular that was “absolutely bad” about FSX. Except the boring visuals. But later REX and OrbX releases changed this problem significant to the better.
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