Now that I have bothered to finish a full playthrough of the 3.0 beta, here are some observations.
After repeated testing, I have to conclude that Drizzle Politoed is one of the better special sponges for most of the main game in the Modified Version. Due to its Water/Grass typing there, it's one of the few 'mons that Lance's damn Wide Lens Multiscale Dragonite can't hit for SE damage with Fire Blast, Blizzard or Thunder, making it a great fit for the Assault Vest item you picked up at Cianwood. The moveset at the time was Surf/Whirlpool/Giga Drain/Ice Beam, although later on I replaced Whirlpool with Earth Power. Muk is also pretty damn good as a special sponge in Modified with the Poison/Dark typing of its Alolan form and Minimize being the cheap tactic it always is, though it has a bit more problems balancing tanking ability with damage output due to how late you acquire Curse and PP issues due to being stuck with Gunk Shot as its only physical Poison attack for the Johto half of the main story and a significant portion of the Kanto half, and I found myself having to use Leppa Berries or Ethers on it in at least a few battles.
I also noticed something funny when fighting Misty. Apparently none of her Pokémon are capable of hitting a Water/Grass dual-type for SE damage or have any secondary typings that make them neutral to Grass, so she ended up switching several times in a row while I had Politoed out and almost never attacked until she was down to her last Pokémon, giving me several free KOs and the easiest win by far out of all of the Kanto Gym Leader fights. You might want to look into fixing the part where she kept switching all of her 'mons out instead of attacking...
Before the E4 rematches, I was reminded of something that is annoying about vanilla GSC. Since it was a Wednesday, I ended up having to fight both Lyra and Silver before being allowed to challenge the E4's rematch teams for the first time in this run. The annoying thing about Silver's final battles is that he uses the Champion theme instead of his rival theme. Would it be possible to switch Silver's final battles' music back to his theme like HGSS did?
The last trainer fights in the game have provided further confirmation of my prior thoughts that the Magnemite and Misdreavus lines are the best non-legendary Pokémon in the Modified Version. The Magnemite line having Levitate instead of Sturdy in Modified enables it to beat the majority of Ground-types with impunity, and its Electric/Steel dual typing is obviously amazing for tanking hits. A moveset of Thunderbolt/Flash Cannon/Thunder Wave/either Reflect or Light Screen depending on which boss trainer you're facing feels like the most optimal set for Magneton/Magnezone to both wreck things and support the rest of your team so they can wreck what it can't. Eviolite Magneton remains virtually invincible against most physical attackers used by the E4 in the first run. As for the Misdreavus line, Mismagius picking up the Fairy typing in Modified after evolution, again, gives it four immunities with only two weaknesses (Ghost and Steel), and coupled with its good Special Defense, gives it many opportunities to set up even with the AI being programmed to ruin your setting up any way it can. Mismagius' Ghost/Fairy STAB lets it hit most of the E4 for super effective damage, and it's one of the few set up sweepers that can take down Green with a level disadvantage (although I had to use an X Speed to make sure it didn't die to Aerodactyl, since even at +6 Special Attack it couldn't OHKO Green's 'mons due to said level disadvantage - it was 88 compared to Green's levels being 95+).
The battle with Green went like this:
1) Lead with Magnezone against her Lapras
2) Set up Light Screen as Mew switches in
3) Tank the incoming Aura Sphere and hit Mew with Thunder Wave
4) Bring in Mismagius to KO Mew
5) Attempt to set up on Lapras but get KO'd by a critical hit
6) Use a Max Revive on Mismagius while Magnezone resists Lapras for a couple of turns
7) Bring Mismagius back in and set up on Lapras, successfully this time
8) Also use an X Speed so Aerodactyl won't outrun Mismagius and end the sweep when it comes in
9) Sweep Green right off the Navel Rock
During the last battles, I had found four issues, all of which were reported last week on the Discord server.
My final team (Levels were 79-82 vs. Red, and 86-88 vs. Green): Typhlosion (starter, though mine originally had Flame Body so I bred a new one with its HA Flash Fire halfway through Johto), Gyarados, Politoed, Muk, Magnezone, and Mismagius. Typhlosion ended up being worthless in the last boss fights and was never brought in. Also, the hax was real in the penultimate fight: Red's Omastar almost never missed with Earth Power against Muk regardless of Muk's evasion boosts (which I had a lot of difficulty even getting to set up Minimize/Curse because of Earth Power hitting so often; once it ran out of clips on Earth Power, it started missing as expected).
After defeating Green was when I decided to go legendary hunting to complete the 'dex (the only Legendary I'd caught before was Suicune, which was not used on my team, and I didn't encounter Raikou or Entei at random in the wild before talking to Eusine in Celadon). My face lit up when I tracked down Mewtwo and discovered that the original Uber now uses an 8-bit demix of Stadium's VS. Mewtwo theme (No, I had not searched through the Music Player for updates to the catalogue prior to this battle). THANK YOU, THANK YOU, THANK YOU FOR INCLUDING THAT THEME IN THIS HACK!
Misc. note on Legendary Hunting - For those who don't plan on using Moltres as part of your main team (or plan on using exploits to get more than one), once you've defeated Blaine and get access to Cinnabar Volcano I would recommend making sure it has its HA when you catch it. Moltres being the only holder of the Flame Body ability in Polished Crystal that can also use Fly makes it the best choice to use to speed up breeding, once it's finally available.
In all, there is no doubt in my mind that once 3.0 is complete, Polished will be the definitive modernization update hack for Crystal. The main game in the 3.0 beta remains too easy due to the current Exp. Share bug and I still remember how challenging certain fights were without the ability to exploit that bug and go into said fights being overleveled instead of underleveled. Also, I am still annoyed by two things (that aren't unresolved bugs/glitches): the lack of space to hold items in your bag's main pocket or PC (Prism currently has room for 60 item stacks in its PC but Polished only allows you to store away 40 item stacks despite having way more items than Prism, and the Medicine/Berry pockets just don't do enough to alleviate that issue), and how absolutely no trainer in the game has Sturdy as the ability on a Pokémon that can have Sturdy as an ability, unless that Pokémon has Sturdy as its only non-HA (and also annoyed by Steelix losing Sturdy altogether in Modified). If you want to make the game even more difficult, addressing the latter annoyance is something that should be done once you have the time to do so.