Worst
#1. Wallace (E)
This fight creates three problems. First, it shoehorns Juan in as the eighth gym leader, making him the second water boss in a region which already suffers from "too much water" jokes. Juan also uses Kingdra as his ace, even though it's a Johto Pokémon already used by Clair as the eighth gym leader in the previous region, making it a puzzling choice. Next, it makes Wallace the champion which frankly he's underwhelming as. He makes a solid eighth gym leader but as a champion he's a type specialist with a team that isn't challenging nor does it stand out. If they were going to do this, I would have even preferred they made Drake the champion since at least he spotlights the other pseudo-legendary of the region, Salamence. Lastly, this exiles Steven to Meteor Falls. I know they were going for the Red treatment from the Johto games, but the problem is Emerald is not a sequel to RS like GSC is to RBY. Continuity wise, it makes no sense. Plus they gave him the rival theme which is not bad in and of itself, but doesn't represent him as he should be as the champion of the Hoenn region. For these three problems I mainly blame Wallace since he's the common thread, but it's unfortunate that they botched the landing of what I consider to be an otherwise terrific game (second only to Platinum on my list).
#2. Lance (HGSS)
If you play the game the "right" way (i.e. Set mode, no healing items in battle, no grinding and only battle trainers for experience) this fight is practically impossible to beat without luck. It's a completely unreasonable difficulty spike without giving you the resources to combat it. The problem is, for this game you have to plan a team to beat both Lance and Red (I prefer sticking with a team throughout the game, rather than renting a Pokémon for a specific purpose only to abandon it) and in this game you have a limited selection of Pokémon to build such a team with. HGSS is plagued by shitty Johto Pokémon stats/placement, inconvenient TM placement, annoying methods of obtaining evolutionary stones/items, and the infamously meager level curve. If you train six Pokémon you'll be around level 40 which is simply not enough to give you a good shot against those Dragonite. This fight is so unreasonable I don't even think if they gave you the TM for Ice Beam before the Elite Four instead of parking it in Seafoam Islands, that it would make that much of a difference. Whoever is using Ice Beam could probably only kill one Dragonite since it'll have to absorb a Dragon Rush/Outrage or one of those strong elemental attacks. Overall, HGSS has its flaws but this fight is the most glaring for me since it's supposed to be this climactic battle that ends up turning into some shitty luck fest.
Best
#1. Cynthia (Pt)
Call it cliché but it is for a reason. This fight is the perfect capstone for what I consider to be the perfect Pokémon game. Platinum, unlike HGSS, gives you a ton of great resources and options to build your team with. But at the end of the day, you still need to build a team to take down Cynthia who probably has the best assembled team of any NPC in the main series. With a team of six you'll probably be around level 50 which makes this fight difficult but not unreasonable, especially given the amazing options available to you in this game, relatively early on. I also love that Cynthia spotlights the pseudo-legendary of the region, Garchomp, which still probably has the most impressive debut generation of any pseudo. Her theme and design are also fantastic. Not much else to say about this fight other than it checks all the boxes and is the best in the series for me.
#2. Blue (FRLG Champion Rematch)
I don't hear this fight get brought up as much. Top to bottom, I daresay Blue's FRLG champion rematch team gives Cynthia's a run for her money in terms of overall quality. I ultimately give Cynthia the edge due to spotlighting Garchomp instead of the comparatively lackluster Kanto starters, but this is still an amazing fight. Blue's theme is also amazing and his cocky personality makes for a great rival. His team's updated move sets are also quite good at covering their weaknesses. With a team of six you'll probably be around level 58 which makes this fight difficult, but Kanto actually gives you decent options to combat him with solid Pokémon and TM availability, as well as evolutionary stones being easily purchasable. Even though FRLG isn't quite the caliber of game Platinum or Emerald is, this fight is certainly a better capstone to the game than the sequence of boss fights Emerald ends with in my opinion.