That's true. I think that it also helps that they've never actually made it clear as to what a Pokemon Master is in the series. Whenever Ash or someone else mentions it, it's like they all know what it means exactly, but the audience doesn't. In the games, it's all about completing your Pokedex. I doubt that it's like that in the series considering when the main characters capture Pokemon, they try to form a bond between them, instead of just mindlessly catching them.
I think another reason why the writers hit the reset button for Ash and his team is so that they can showcase the most recent generation of Pokemon on his team. He did lose to Drake, one of the Hoenn Elite Four merabers, back in Advance Battle as well. As for the Orange League win, I think it was still impressive since no one defeated him with Dragonite before and we don't know how long he had remained undefeated.
Back in season one, I think about half of the badges he won were out of his skills as a trainer, the Thunder, Soul, Volcano and Earth Badges respectively, and the other half were basically given to him. I prefer the current gym battles too. The only way I see those battles being repetitive is that Ash almost always win, except for the occasional loss once or twice a region, but even so, he pretty much always uses a different set of Pokemon for each of his Gym matches.
I also think you bring up a good point about the Indigo League. While I find it enjoyable to watch after not seeing it for a long time, I wouldn't consider Ash using strategy in those matches for the reasons you mentioned. While Ash used his skills in those matches, he was still kind of a rookie and I thought most of his victories were really weird, especially his first match with his Kingler suddenly knowing Hyper Beam. I'd honestly take Ash's Hoenn and Johto matches over his matches in the Indigo League.
I thought that Ash did try a bit more during the Orange Island saga to get Charizard to listen to him. Though, that was mostly out of force/begging rather than befriending it. At least until the episode where it did listen to Ash. I'm not sure if I would count catching Primeape like he did as saving its life. It did show Primeape how Ash cared about it, but it wasn't much since he gave it away during that same episode.
One could argue that Team Rocket looked and acted more like serious villains in their very first appearance and their character designs did make them look more intense as well. However, I don't think that they were meant to be taken as a serious threat. It's kind of hard to do that since they lost to a Caterpie in episode three, chased and stung by Beedrill in episode four and then kept on digging holes throughout episode five. Plus, if they were really suppose to be intimidating, I don't think that they would almost always say their motto before trying to get Pikachu. I also believe that there have been times in the recent seasons where Team Rocket tries to steal Pokemon that don't belong to the main characters.
As how I feel, I like the first season and I have the three Indigo League box sets. The season is enjoyable to rewatch since I remeraber watching it back in the day on KiRAB' WB. However, I don't think that it's the best season out there. It was a nice first season, but I felt like aspects of Pokemon, mainly how the group of trainers and Pokemon are handled with their different personalities, have gotten better with age. Back in season one, Ash only used Pikachu and the three starters. Pidgeotto didn't really have much screen time, which is too bad since I like the Pidgey line. Nowadays, more of his Pokemon have fairly equal or close to equal screentime with some personality and maybe even a good background story. One of my favorite parts about the Sinnoh Saga is Chimchar's story. It's so good, yet so sad.
Outside of Charizard vs. Magmar and Pikachu vs. Raichu, I didn't think that there were that many memorable battles in season one. I've enjoyed watching more of Ash's Johto, Advance and Sinnoh matches since he actually uses his skills as a trainer, as apposed to getting a badge for free. In fact, I enjoyed his Gym match against Lucario more than the Indigo Gyms, though I'm probably biased since I love Lucario.
As for Gary, I didn't think he was much of a rival. All he would do would show up every now and then, insult Ash's skills as trainer and then leave. Back then, it felt like a rivalry, but now, it feels more like he was just being mean to Ash. We didn't even see any of Gary's Pokemon until The Battle of the Badge episode and we didn't see a battle between Ash and Gary until the end of the Orange Island saga. That doesn't feel like much of a rivalry to me. I liked their battle in the Johto League, one of its highlights in my opinion, but I feel that Paul is a better rival than Gary ever was. At least when Paul shows up, he does more than just insult Ash. We've seen his skills as a trainer and they have battled like three time already. I think that it also helps that Paul is pretty much the polar opposite of Ash, which makes really intense interactions when they meet up.
I like how more of the characters have more screentime/action than they did back in season one. Even though Misty was more active back in Kanto than she was in Johto, I feel like she could have done more than she actually did for some reason. Plus, the only remeraberable Pokemon that she had back then was Psyduck. As cool as Brock was back then, I don't think that he had an active role either and he didn't really have much a remeraberable team either. At least in Hoenn and Sinnoh, I feel like Brock has gotten better screentime, even when he's more like the side story within an episode. Even Max had a nice bit of focused every now and then.
I also loved how May developed from a girl who didn't even like Pokemon to one of the best Coordinators around. It felt like a realistic kind of development for a Pokemon trainer. Even though I don't like Dawn anywhere near as much as I like May, I do admit that she at least tries in her efforts to develop a bond with her Pokemon, which worked to get her Mamoswine to listen to her.
I love Pokemon and I've watched the show for over ten years. As much as I enjoy watching the Indigo League season, I believe that Pokemon's writing and focusing has improved over by age. Of course, that's just how I feel and it's understandable and expected that others feel differently about this matter.