Chapter Discussion Oda not making sense by having Who's who going to jail.

Simple: Who's Who might've been the highest ranking agent when guarding the Gomu Gomu no Mi, while the Enies Lobby incident was Spandam's responsibility.
The only reason why Lucci and the others were chased is because Spandam and his father used their power, but I guess the higher-ups stopped that during the timeskip. And the reason why Spandam isn't in prison could be because Lucci used his new rank to make his former boss his subordinate.
It depends on what the World Government was transporting the fruit for. We know the Celestial Dragons are advent collectors of Devil Fruits, and they love to feed them to their slaves for entertainment purposes.

If the fruit was bought by a Celestial Dragon, and WsW was responsible for losing it, then it would make 100 percent sense for him to get jailed for it, because Celestial Dragons are pieces of shit who would kill someone just for stepping in front of them when they are out for a walk.

That's just on example, but there could be a multitude of other reasons as well. We don't know the full story yet, but I'm sure it will be revealed in due time.
By the way, although I explained how it could make sense that Who's Who went to jail and Lucci didn't, I can't see how the Who's Who thing on its own will make sense.

Because on one hand, the Gomu Gomu no Mi must be important enough to get escorted and also to throw someone into jail because it was stolen.
But on the other hand, it seemingly wasn't important enough to let a CP-0 agent or an admiral do the job. Maybe that would've given even more unwanted attention to the fruit, but still... kind of wonky argument.
If I had to guess... Lucci had the rest of the CP9 protecting him post-Enies Lobby (from the cover story), which is why he didn't get captured. WW, on another hand, was presumably working alone. If WW had friends among the CP9, they could have helped him just like in the cover stories.

Another thing is, Lucci probably told the truth about the EL incident to his higher higher-ups so both him and Spandam were to blame, but Aokiji as an admiral is a laxed creature so he probably gave no punishment to CP9 cuz he took the blame for everything, which can be used to explain why the WG vouched for Akainu instead of Aokiji when choosing for the next Fleet Admiral.
Wtf are you all talking about? Marines did send troops to capture Cp9 after ennies lobby. There was an entire cover story about it.
Obviously sth happened later and changed their mind, but their initial reaction was the same as in who s who's case.
Also Who s who wasnt in jail for 12 years. He was a pirate captain before joining beasts pirates. So he must have been a captain for at least some time.
This thread doesnt make any sense. I think some of you just looking for excuses to trash Oda.