OK starting a new list.
1. The Third paragraph in the initial hail should be colored green.
2. I like the dialog when you enter the mission but it is worded rather strange. Consider rewording it something like this. 'Iapetus welcome to station (I forget the stations name). Dr Val Kellian has been expecting you. We are sending navigational data for your approach.'
3. When you are first contacted by Vel my option is to respond with 'Not just let.' It should be 'Not just yet.'
4. I found the briefing to be hard to read. You might want to look at the formatting. Also it might be a nice touch to add an optional dialog box where I can ask about who Dr Thallien is. If you do add optional questions make sure you make the choices that progress the dialog chain as green.
*spoilers*
5. Finished the mission. you may want to review you dialog. I get what you are going for here but I never really felt betrayed. I never really got to know Val. This was a big disconnect for me. Since he is central to the betrayal plot the player needed some information on who he was, or at least who he was saying he was. Hints along the way starting from the mission accept screen that give you clues on why Starfleet is trusting him and what his actual job is. It would set up the betrayal/trap alot better.
I also felt uneasy about the choice to make him a Solone and the Aretype Tholion also felt strange. The Aretype guy could be left a mystery for use in a future episode. Who is he, what are tehir goals, What is their relationship with the Tholians. IT would be really interesting to explore those topics in a seperate mission with this as the setup. As for Val being a Solone. I feel like you are treading on Cryptics toes a little. The Iconions and Solone are important parts of the emerging plot for STO. While I understand your desire to use them it might work better if Val is a Subserviant race that is using Solone technology. That would open up new area of mystery. Why are they using Solone technology. What is their relation with the Solone. Make him a unique race that you can expland on in future stories.
Actually fighting the drone fleet was fine. I like the idea of having shops of different races fighting you. A few recommendations though
In the initial briefing you might mention tha tthe drone ship is already gathering ships. You can do this by rewording the description of what the Andorian Suite is. In the briefing describe what it was supposed to be. Then describe how it is gone wrong. Finally talk about hwo it is already amassing ships to give the mission urgency.
When you spawn into the system where the fight takes place you are placed in the misddle of the fight. Give the player a chance to analyze the situation and then move in to attack. On warp in have the science officer make his comment then about how strange it is to see Tholian ship here. Some dialog about how they seem to be fighting the drone ships might be useful as well. I thought that it was a bug they were fighting each other until I got to the last dialog box.
As to your question on weather you should make it longer or make a part 2. I would recommend a part 2. Let this be the hook. There is some combat and the potential for some interesting new races to discover if you work it right. Its not a super long mission which is something I like in a Founfry mission. It hit just the right amount of length for me.
In future missions I would like to learn more about the two races you have created in this mission.