First of all, I want to thank you very much for commenting and sharing your opinion on the project.
I'm trying to use as many KSP parts as I can, with the minimum modification. But I want to make that extra step into realism, and for that I need to make some changes.
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Talking about the part mods, these Blender models I'm working with are very high poly for a game engine to handle. Of course we could cheat the system with baked textures but we must realise that details sell the product. All those pipes, lights, pistons and balls I added is what it really makes the engine look nice. That added geometry goes in decrement of the game performance... a game in which performance is not its greatest achievements. So unless the modder invents some kind of modding magickery, it's not gonna be possible for the parts I made to be ported into the game.
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About the engine bells, I have reasons to leave them as they are. Although what you say about the Poodle not being suitable for atmospheric operation is true, we must recall that Duna's atmosphere is very thin and has 1/15th the pressure of Kerbin's atmosphere, practically vacuum. That combined with the reduced gravity of Duna, makes the poodle engine a considerable option. I've been using this model in the game for a while now and it works like a charm. Could it be more efficient? yes, sure... but what the hell... it gets the job done. I can get from the surface of Duna to Kerbin with it. Picture on the right.
I'm also leaving the poodle engine as it is for storytelling reasons. The mission commander will interact with the engine bells and the size adds to the story.
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I hope we can further discuss about stuff, I really enjoy community involvement. Don't forget to send me a flag design if you want, or the kerbal names.