Why not 3 elements for free then 1 pnt for each one thereafter?
That sounds like a decent idea. Working along refinement lines there.
Allowing specialization might help too
Edit: expanding on that. I don't see why tinker's can't specialize. It's even a part of the Fiction: each Tinker had his/her Niche. Why not take some categories from the list and let them specialize.
So speciality +1 complexity(size decrease); +1 complexity (Encryption); +2 Power (Area)
So you get a rebate for items with those specialities. It has to follow the speciality pyramid, as normal.
Let's take a quick look at this.
With the current system a Submerged Tinker can have an optimised set up like so:
Skills
+5 - Capes
+4 - Scholarship, Craftsmanship
Powers
Tinker [-3]
Refinement [-6] (Focus Items +8, Enchanted Items +8)
Focus Items
Complexity - +4
Power - +4
Frequency - +0
Devices
Complexity: 8, Power: 9, Frequency: 4.
Tinker Gun (Guns)
Complexity: Element (Force) [0pts], Size Decrease -3 [3pts], Frequency +2 [4pts], Encryption [1pt].
Power: Effect (Stress +9) [9pts].
Frequency: 4
Size: 6 (Rifle)
That's one of 8 different items a Tinker can have. Other examples could be a set of Power Armour with +4 Armour for a total of 16 hits (+4 Frequency, +1 Duration), a helmet with +9 skill replacement for Guns, and so on. Pretty powerful, and batteries work much more effectively than fuelling items with mental stress does in the RAW for Devices that require frequent usage.
Now if we look at a specialisation set up (optimised for the highest possible power):
Skills
+5 - Capes
+4 - Scholarship, Craftsmanship
Powers
Tinker [-3] (Specialisation +1)
Refinement [-6] (Specialisations +12)
Specialisations
+4 - Power (Effect)
+3 - Complexity (Size Decrease)
+2 - Complexity (Frequency)
+1 - Complexity (Encryption), Power (Duration), Power (Area of Effect)
(I'm taking this to mean that specialisations would give a buff to the effect itself, rather than granting extra points to spend on the entire Complexity/Power list. Those would be left equal to the applicable skill rating).
Skill Points
Complexity - 4
Power - 5
Frequency - 4
Devices
Tinker Gun (Guns)
Complexity: Element (Force) [0pts], Size Decrease -7 [4pts], Frequency +2 [0pts], Encryption [0pts]
Power: Effect (Stress +9) [5pts], Duration +1 [0pts], Area of Effect +1 [0pts]
Frequency: 4
Size: 4 (Handgun)
So a Tinker with specialisations could replicate the effects of a Tinker with Focus Items (with a bit of a bonus), but only in one area. That's... a good idea, though it does a bad job of modelling characters like Leet, who are fairly low in skill points, but high in refresh using this system. Then again, Leet probably has a huge Limitation attached to his refinements.
I think I like your system more than the current one. We'd need a write up for it first though. I'll have a go at it later. Might have trouble incorporating the specialities that don't have numerical bonuses attached like Inflicts Mental Stress [3pts]. We'll see how it goes.