I have said from the beginning that Stussy is still on the WG's side (It was her, who had called Akainu and informed him that Luffy was on Egghead, without having to - this made it near impossible for Vegapunk to flee). And now Lucci has made a move and stabbed her and is now viewed as an enemy by all. An enemy that can be left behind - I still don't know why, though. Additionally he has eleminated Stussy, because she was a thread to Vegapunk and their escape.
If you want to see the connection Lucci has with Vegapunk, you have to compare Shaka and Lucci together. Because if you do, you will soon notice that both characters are twin-like counterparts. Everthing! Even their names are mirror-like aspects of each other.
- Both are constantly seen shoving their hands into their pockets
- Both are always calm and collected, even if the situation is dire
- Both are proficient strategists, who their comrades like to turn to, when a problem arises
- Both are ready to sacrafice everything they have for their main-goal (Shaka saving Vegapunk; Lucci getting Robin back, because she could activate the ancient weapon the world fears)
- Both of their names refer to a god-like personification: Shaka = Buddah Shaka Nyorai (Japanese religion) as the personification of good; Lucci = (as a short form for) Lucifer as the personification of evil
- All three, Vegapunk, Shaka and Lucci do not like pirates, with Lucci even strongly detesting them
- Vegapunk and Lucci are sharing the same dream: Peace (Vegapunk through his discovery of the energy-source and Lucci was drawn by Oda as a child with multiple symbols for peace (white dove, olive branch and on his shirt the word "peace"; Lucci even stated in Iceberg's bed-room that he wants to free the people of the thread the pirates pose.)
These small tid-bits are so numerous that it makes it impossible for me to ignore them. There is a connection and Oda is still hiding that. Hell - think about the time-skip and why Oda inserted it here: He clearly wants to hide what was going on between Luffy and Lucci and wanted to hide us seeing Chopper arriving down in the basement, only to find out that Shaka looks like Lucci as he pulled off the helmet of his to start treatment. Why it is there in the first place needs to be speculated strongly.
God, there is so much that does not fit - and here I'm rambling again ... .