Once I could ditch multirole and afford dedicated ships things got much better! Elite ships are modular and that's a good thing. You can swap modules in and out as the mission profile calls for. Works fine but it's a pain in the neck. Especially mining ships. Not only are you swapping optional slots and utility slots, you're rejigging priorities and fire groups. Bah! Who needs it?
Well, commanders on a shoestring do. But keep building that bank so you can afford to dedicate a ship to each role you perform.
To answer the question, I'd say the two most important parts of your ship are shields and thrusters, so I'd start there. And FSD, which everyone engineers first. Get those three things done straight away and the rest can fall in to place over time. Mock it up in Coriolis so you see what your final power requirements will be.
I have at least three Krait IIs, each with a defined role. Always ready, no swapping required.
My combat Krait. Used to prowl CNBs, RES and CZ to engage in combat and sweep up the mats left behind.
Poison Whiskey
My transport Krait, I call it a rumble bus. For bulk haul and VIP transport, occasional rescues. Armed to give the interdictor the good news.
Parabellum
My mining Krait. I'd rather poke sticks in my eyes than laser strip mine, and this boat is set up for core mining with the occasional trip with drill rockets to dig out the tritium.
Twin Reverb
Each of these is quite different in build, as the roles call for. My build philosophy is fast, cool, light weight shield tanks with good jump. Integrity and firepower are often what I need to give up to get what I want. No ships in my entire fleet have armor save heavy duty stock alloy bulkheads and HRPs (HRPs are gold the way the resistances stack). Speed is life after all, cool temps give you some margin and well-engineered shields provide the final failsafe against destruction.