Gen 3 is solid, but not what I would call the "best". I would say it was basically 2 steps forward and 1 step back, there were a lot of massive improvements here but also a lot missing from GSC. Looking back I have a great appreciation for what Gen 3 brought to the series, but at the time there was definitely a sense that it felt like a part of the series had died (even though it really didn't, but we didn't know at the time that later games would bring back the things that RS had dropped).
First with RS, the game brought a lot of major changes such as abilities, natures, double battles, the Running Shoes, berry planting. New side modes such as Contests and Secret Bases added a sense of replay value to the series that was largely unheard of. Even simple changes such as being able to walk under bridges or behind buildings blew my mind (I totally missed the berry patch on Rt. 110 that you had to walk behind Lanette's House for because I had no idea you could do that, I thought you needed Surf to get there and the berries dropped to the ground and reset so I had to wait even longer to pick them) because you could never do that in previous Pokemon games. The games really felt worthy of the Game Boy Advance because these games were very much advanced Pokemon titles over their Game Boy counterparts.
And yet, there were a lot of things missing. Compatibility with the Game Boy games was completely cut off leaving the precious Pokemon we'd spent so much time training and bonding with left behind. Worse yet, about half of the Pokemon weren't even in the game at all when the GB game had every Pokemon (aside from some version exclusives and the Gen 1 starters, fossils, and legendaries in Gen 2) that existed at the time available in the game, feeling like a mini-Dexit scenario. The old regions were completely gone whereas Gen 2 had every location that existed in the series. Day and Night were no longer there. It might seem unreasonable to have expected many of those things but these were things that Gen 1/2 players were used to so them ending up missing was utterly gutting.
There's also a couple of other flaws unrelated to past games. Post game content is really poor in the base RS, it's very RBY-esque with just an extra dungeon containing a legendary and a ship that leads you to a Battle Tower. One of the worst post games in series history for sure (only RBY, LGPE, and XY are comparable). And like all early gen games, there was a lack of variety of some types of Pokemon. Ice, Ghost, and Dragon were definitely lacking in this game. To be fair, there wasn't much they could do at the time because the entire National Dex was lacking Ghost and Dragon (they certainly could've thrown a few more Ice types into Shoal Cave though), so this is more something that hasn't aged well than something that they simply made a mistake in designing, but it's still a pretty glaring flaw that would make it hard for anyone used to more recent games like BW2, XY, SM, or SwSh would find lacking.
Skipping ahead a few games to Emerald, it did fix a few of the flaws with RS. The storyline made a lot more sense now, with both evil teams trading off different events wherever they made sense instead of one being evil and one being good for some reason. It addressed the issue of not having a lot of post game content with new areas, adding in areas such as the Safari Zone Expansion, Desert Underpass, and Terra and Marine Cave and filling them with National Dex Pokemon that were otherwise exclusive to Colosseum/XD giving people that didn't have a GC an option to catch those Pokemon. And of course no discussion of Emerald would be complete without the Battle Frontier, the Battle Frontier was a big deal at the time and was promoted hard in Emerald's release (it even got an entire season of the anime around it). The Battle Frontier was a tremendous upgrade over the Battle Tower that added a lot of new battle facilities with unique gameplay styles. It is a little tough to get into if you're not competitively minded, but the styles were fun and the games that don't have a Battle Frontier (or at least some well-varied equivalent facility like the PWT) feel lacking. But the rest of the flaws remained unaddressed (and there really wasn't much they could do).
Back to FRLG, these games were remakes of the classic RBY. And what was good about RBY was also good about FRLG. Several of the cut Pokemon from RS returned, making it clear that those Pokemon weren't gone, just slowly being reintroduced to the series. And they even added a new post game campaign in the Sevii Islands (which seem to be a pseudo-Johto to compensate for Johto not existing in Gen 3 at all with tons of Johto Pokemon and remixes of some Johto music) with new areas, new Pokemon, and extra side modes. They did bring the games up to speed mechanic wise adding mechanics from Gen 2 and 3 such as hold items, Dark and Steel types, abilities, and natures, but other than that, it was mainly the same game. The same selection of 151 Pokemon (until you get the National Dex in the post game). The same region design featuring the same flat, short, dull, simplistic designs of RBY which felt like a step back from the environmental and altitudinal variety of RS' terrain. The same lack of depth to the story and characters when RS had a much more coherent and overarching story with more impactful characters that have legitimate motivations beyond "just beat you in a Pokemon battle" or "rule the world". The same lack of QoL features like a regional gadget (although it did have the fantastic Vs. Seeker which was and still is the best rematching tool in the series but other than that it just added the largely useless Fame Checker). They could've done much, much more to modernize FRLG and they just didn't, and IMO that's set a bad precedent for future remakes (HGSS and ORAS did improve them in other ways, but even they still feel lacking compared to their current gen cohorts).
Lastly, with the generation as a whole, this generation handled mythicals very poorly. They were mandatory for completing the National Dex, but they weren't very accessible, leaving many people unable to complete their National Dex through no fault of their own. Many of the mythicals required you to attend real life events in only a handful of locations, so if you lived in the wrong area you were basically screwed (I myself lived in Baltimore and there were no events anywhere near there in the U.S.). There were no Wi-Fi events and largely no in store distributions (IIRC, there was one for Mew, but I was not on the internet that heavily during Gen 3 and was never made aware of it), you mainly only got them if you happened to live in the right part of the world. So my National Dexes in Gen 3 are just sitting with a handful of blanks that I can't really do anything about (aside from less than legitimate means).
Ultimately, they were good games, but they have their flaws and there's better ones. In particular, I think Gen 4 is a much more polished version of what they were trying to accomplish with Gen 3 and that's the generation I would say is the best one.