Athens is surely a nice city with a vivid night life, museums etc.
But the fact that it's so crowded and noisy makes it difficult to live in and sometimes faceless. For people in Thessaloniki, Athens is considered a good destination for vacation (3-4 days) mostly because of the music scene that's stronger there but I personally think more days will get someone easily tired.
When it comes to the public transportation you have many options compared to Thessaloniki but the truth is in Thessaloniki you can easily live with less if you enjoy walking (unless you want to reach more difficult areas). The city is way smaller than Athens and I believe it keeps a more traditional character. There are many many students, many kinds of night life (clubs, bars etc) without the need to travel hours with the bus. If you enjoy food, Thessaloniki's little streets and places (like Ladadika) will give you the joy you're looking for. And if you're more athletic a morning run at the beach feels great.
And my favorite part is..You take the bus and in 30 minutes from the center or less you get to Kalamaria. A beautiful region with a nice little sea port, perfect for a morning coffee.
For any questions feel free to ask.