All of these are valid, but you can also say あいたかった lit:"I wanted to meet you" but usually means "I missed you"

あなたと一緒にいたい。

あなたがいなくて寂しい

I think that "あなたと一緒にいたい" imply "あなたが恋しい", "あなたに会いたい" and "あなたが居なくて寂しい" in my sense.

I love questions like this because I want to see how people respond hahaha There's no direct way to express that in Japanesse. Because you're not here, I'm lonely. I want to see you. I want to be with you. So, if the person you are speaking to also speaks English, sometimes English is the best choice. That's the benefit of being able to speak multiple languages, you can choose the most fitting language for the situation :) The point of learning languages is for communication, after all. So I generally just choose the clearest option. If you're insistent on using only Japanese, then feel free to use a Japanese equivalent. But keep in mind that it won't always have the same effect.