Ash. Misty, and Brock: The original trio definitely had some great chemistry. You could tell they were all great friends. There was lots of interaction between them, but a good portion of it was fighting. <_>
Ash, Misty, and Tracey: Probably the second worst group as far as chemistry goes. Tracey was almost totally ignored.
Ash, May, Brock, and Max: Not only was this my favorite set-up, but I think the had the best chemistry as well. They all seemed to just click, and they all felt like family. No one was completely ignored either, unlike Brock in DP. I particularly loved when the four of them would split up into two groups for an episode. The fact that the 'teams' were mixed up all the time backs up my point. In DP it was always Ash and Dawn going somewhere while Brock was totally shunned. Everyone interacted with each other and you could really feel their bond.
Ash, Dawn, and Brock: Personally, I find this trio to be the worst. Ash and Dawn eventually had a boring friendship, but friendship is friendship I guess. The real problem in this group was Brock. Brock wasn't the problem himself, he was just totally shunned by the writers and even his friends. Ash talked to Brock at times, but not nearly as much as he did in previous seasons. Dawn completely ignored him, it was like he was never there. The only time they would talk was during gym battles, probably to make things less awkward.
Ash, Iris, Cilan: The fact that Brock, Ash's best friend (Practically his brother.), is absent hurts this group's chemistry as of now. There's nobody Ash really knows in this group, yet. When BW started it was like Ash didn't even want to travel with Iris. He's going to need more time to adjust to green-hair and jungle girl before I can judge this fairly.