Yes, Beethoven's instruments were different. A big example is when Beethoven calls for the damper pedal to be held down on the piano for extended periods, which means the strings are allowed to vibrate until they stop on their own. Try that with a modern piano, and it sounds like mud from all the different notes that are played within a short time. But his piano strings didn't vibrate nearly as long as ours do. Even later, Liszt would break the keys and strings during performances. Sure, he did it intentionally, to WOW the audience (the women used to have fistfights over the cigar butts he left behind), but just try to break them on today's piano. (And again, after Beethoven, Schumann called for the newer style trumpets and the older ones to be used at the same time, because they set up some kind of resonance, or something like that.)
I'm crazy about the 9th performed by The Academy of Ancient Music, conducted by Christopher Hogwood. As I was checking amazon for the disc I have, I see that the complete symphonies by this group are available for $36, on 5 discs.
www.amazon.com/exec/obidos/ASIN/B000004 ... 38-7807250 I'd absolutely get this if I hadn't gotten most of the individual discs when they came out.
Then there's Roger Norrington conducting the London Classical Players. Their complete symphonies
www.amazon.com/exec/obidos/tg/detail/-/ ... =classical is $34, and also very good.
As for why the symphonies are paired the way they are, it usually has to do with running times. Some compositions didn't fit in the 80-ish minutes that they could put on a disc at the time. Other times, if any two of four pieces could fit together, they'd try to team them up so that the total times would be about the same. So instead of two 40-minute pieces together, and two 30-minute pieces together, they'd have a 30 and a 40 on each disc. I suppose there might be other reasons too.