I wouldn't have altered the flow of the show much in terms of seasons (except Season 4, which I wouldn't have incoporated that witch storyline). Here are some of my thoughts:
-The Veritas group would've been around from the beginning of the show: In addition to the Luthors, Queens, Teagues, Dr. Swann, the group would've also included the Waynes and Kords. In addition to the freak of the week, Clark would've had to face off against the various families and their minions. Not all of Veritas members would be bad (i.e. Waynes) though and some might want to help Clark and not exploit him (Dr. Swann). I would've had Bruce Wayne visit Smallville (not Adam Knight) as part of the Veritas storyline at some point.
-Took Lucas Luthor-idea and made that story Tess's introduction. Then she could just return in a later season. I don't think knowing who she was from jump would hurt her redemption arc. It might strengthen it. Also, Tess's ties to Checkmate would've been far stronger. She would've been a Checkmate agent upon her reintroduction.
-Regarding Checkmate would've liked CCH Pounder for Amanda Waller, or Garcelle Beavious (sp).
-Made the Jor-El A.I. actually be General Zod's consciousness, which had infected and taken over the A.I.'s programming. He would be trying to control Clark, and when he couldn't turn Clark into his loyal footsoldier he would tried to use him as a vessel for his phantom. I wouldn't have done the Lex-Zod thing. Either Clark, a clone, or the actual physical Zod. Maybe had Gerard Christopher play him.
-I liked Erica Durance but I would not have made Lois a major character, at least until the last two seasons or the last season. Maybe even close the show with him meeting her, or meeting again after a very long time.
-Brought Steel onto the show in a one shot or two parter, as Metropolis's defender, who teaches the Blur some lessons on heroism (in opposite to how it went down in the comics). Even imagined D.B. Woodside for Steel. Would've had Natasha Irons become a recurring character. I thought Kandyse McClure would've made an interesting choice.
-Brought Mercy onto the show as Lex's bodyguard.
-Perhaps in the first season, would've introduced the Prankster. And at some point, Titano. Other villains I wouldn't have minded seeing are Kryptonite Man, Atomic Skull, Livewire, Eradicator, Manchester Black, JaxUr.
-Would've done more with Metallo. I think he could've been a season-long villain. Same with Bizarro. Also done more with Parasite and Intergang.
-With Darkside might have used the Club Darkside angle from the comics as a way to introduce him. Had Tony Todd playing him.
-With Suicide Squad, I wouldn't have made Deadshot a cowboy and I would've used them a bit more.
-Used the term metahuman at some point. I would've preferred that the anti-vigilante movement be an anti-metahuman movement.
-Would've had Lana leave after realizing that she loved Bizarro-Clark more than the real deal. That Bizarro in his own way was more honest with her.
-Chloe would've died in Season 6. Sorry.
-Brought in the real Krypto.
-Brought in Hank Henshaw, if nothing more than a cameo.
-Supergirl would've worn the "S" on her chest.
-Blur would've started out wearing a mask, but saw that scared people and made him seem like he had something to hide, so he eventually takes it off.
-Lex would've turned fully dark much earlier and his murder of Lionel been a bit more declarative, more jolting. Just felt it was handled sort of blah.
-Kept Green Arrow on the show, and kept him the Bruce Wayne figure, but would've brought in more things from his comics, like Merlyn (by name), Shado, etc. Also would've developed the Black Canary relationship more.
-In the finale would've shown the Justice League also in action. Also with the finale, I would've spent the finale two hours on the big, global battle to save Earth, and not wasted one on a wedding that didn't happen. Clark would also be in a physical supersuit.
-The big fights also wouldn't last two seconds after a season-long buildup.
-Would've found some guest spots for Stacey Haiduk, Sherman Howard, and Gerard Christopher. I thought Smallville did a good job bringing in actors from the films and Lois and Clark, but wish Superboy had gotten a little love.