I started playing the Pokemon games around Emerald's release and entered the online fandom in the midst of D/P speculation, so I don't have any sentimentality about the anime's original season. The first ep I ever saw was an Indigo League ep, yes, but I'm not biased towards that season.
First off, I hear a lot of people (including Lukeex059, my own informal pair on FFnet) say that the show got bad after Misty left. Is that well-founded opinion or attachment to a character? I think some folks got resentful towards May and Max because they 'replaced' Misty. Well, here's my take on the situation; I actually appreciated Misty more after she left. Her appearances in Chronicles revealed a side of her personality that I hadn't seen often - the calm, confident, responsible Gym Leader. If May and Max were replacements, they were good ones. You can't fault May for being a novice; she just started training, folks. She's bound to mess some things up. Opinions of Max vary, but I have a soft spot for nerds. Having someone in the posse who isn't a Trainer was an original spin on things. And May and Max's entrance switched up the roles in the team, too, having May as the novice and Ash as the mentor (even though he still didn't have everything down.)
Obviously the new animation is better, and you can't fault the old season for having crappy graphics. But although it really isn't a valid comparison point, I personally enjoy watching the newer, more graphically pleasing episodes and movies.
Voices...honestly, I don't know what everyone's so worked up about. The new voices are different, but they're not awful. I'm not a huge fan of Ash's voice (Veronica Taylor's performance in AG was my personal favorite) but the new VAs have improved since the anniversary special. In fact, I rather like James' new voice.
Aaaand story quality. I'm probably going to take a few bashes for this, but...the original season bores me. It's just filler...filler...filler...Gym battle (and cheaply won badge)...Pokemon capture...filler...you get the idea. Most - if not all - of Ash's badges were either pity badges or won through some ridiculous, Mary-Sue-ish twist of luck. The Pokemon captures were fairly predictable (he ended up with a full team of starters. Tell me how that isn't cliched.) and the stories surrounding them were a bit weak (Ash protects Squirtle ONCE and he turns from a life of crime? Wha~?) And over half of the dialogue was cheesy/corny/stupid/just not funny.
In Johto, the Mary-Sue-ishness was turned down, thank Arceus. And some of the fillers were pretty good (-cough-Forest Grumps-cough) There was still a spattering of stupid dialogue here and there, but not enough to make me hate it.
Then we come to Hoenn. IMO, it was about on-par with Johto, except for one thing; Contests. I've heard people groan about how boring they were, but I have to disagree heartily. Having May and her Contests serve as a distraction from Ash's badge quest freshened up the series for me, providing an opportunity for some between-Gyms eps that weren't filler. And besides; if we didn't have Contests, we wouldn't have Harley in all of his freakish flamboyant awsomeness! :D
And now we're at Sinnoh...and I must say, I'm impressed. The characters, while nothing special, seem a bit more realistic to me. A lot of the jokes are actually making me laugh. There are non-Gym, Contest, capture, or evolution episodes that actually contribute to the plot! Specking of the plot, it's actually - wait for it - gaining some semblance of continuity! Things from previous episodes are referenced in later episodes (Misty Lure!!), characters are recurring (Hunter J ROCKS. Period.), and there are hints of foreshadowing (A Secret Sphere of Influence, anyone?)
So as my final verdict, I say...all of the seasons have something going for them, but I prefer the newer episodes to the older ones. I can understand that some people feel sentimental about the original season, but...I don't.