I am going to do a short review of both seasons to determine which is best.
Now in the part of the episode ratings, i will go off what i feel the general consensus of the episode.
S1- Top tier episodes include the Gas Mask 2 parter, Fathers Day, Dalek, The finale
S1- Good/Solid episodes include Rose, Unquiet dead
S1- Average episodes include End of the World and the Slitheen episodes. I believe even though the farting is ridiculous, the story itself still has a lot of merit.
S1- Bad episodes include The Long Game
S2- Top tier episodes- Girl in the Fireplace, (arguably the beast 2 parter, but i think it is just a tad below top tier)
S2- Good to top tier- The beast 2 parter
S2- Good/Solid episodes- The Finale, Idiots Lantern, Tooth and Claw, Cyberman story
S2- Average episodes- New Earth, School Reunion
S2- Woeful episodes- Love and Mosnters and Fear Her are generally considered in the worst of Doctor Who, not just the new series.
The first season was a lot more raw and real with heavy hitting episodes with emotional payoff. And the Doctor, Rose, Mickey all worked very well in season 1. And Captain Jack was great in his cameo.
The second season for the most part was definitely more light and chilled, now in this season i despised Rose as a human being. This comes down to the relationship with The Doctor changing, and now she treated everyone horribly. So much so Mickey left to a parallel world.
So, Season 1 had the stronger episodes with more consistency in its episodes, and the character development, interactions with each other were done far better.
So Season 1 wins, comprehensively.