Half of those problems are unique to GSC and got carried over to HGSS.
BW/B2W2 alleviated the HM issue tons, you're rarely forced to use them.
As for status attacks...without them the game is literally just about OHKOing the enemy. :L
Welcome to Gen 2, TC, GSC definitely had its issues. For me, it's the region I like the least.
// prepare for opinions //
Go pick up White/Black/White 2/Black 2, they're FANTASTIC. W/B even have a great plot!
Third gen. Hoenn was FANTASTIC, seriously, it's really great. They haven't remade a 3rd gen game yet, and being older cartridge games, save batteries are starting to go on the poor things, so getting a copy might not do you much good. There are so absolutely fantastic ROM hacks though.
Fourth gen's Sinnoh was also quite good, but not as good as third, if you ask me. (HG/SS are 4th gen games, btw, and incorporate the Physical/Special split as I'm sure you know by now).
And, again, fifth gen's Unova region is just great. It's not without flaws (Dream World, I'm looking at you), but it's really quite good.