Hmmm lot of interesting perspectives in here.
The first thing you really want to figure out is if you want to spam Siege Pulse for combos or just get along with pure weapon damage. I probably prefer the former these days.
Really I think the only 3 skills worth maxing all the time on the Juggernaut are Siege Pulse, Juggernaut, and Hardened Platform. Then decide what sort of split you want between Hex and Turret. I prefer either all Hex for Pulse, Shock, Large, or 4/4 Pulse and then Restore. You can do 5/3 as well.
For Siege Pulse, you want Damage, Protection, and then Rank 6 sort of depends on if you want to spam SP or use pure weapon. For pure weapon, go the increased shards. For SP spam, most recommend the Resistance evo so each SP does more damage, but I don't think it matters much. You can set off an extra combo per SP cooldown cycle with the number of shots. But the Resistance evo should be a "multiplicative" damage bonus to the specific defenses and will do better damage against protected units. It is up to you.
In the Juggernaut passive, just go all weapon damage evos (4a,5b,6b).
It makes sense to me to max Hardened Platform regardless of the style you want to do, unless possibly if you are going pure weapon, then you may want to just stop at 5. For siege pulse spam I prefer all durability evolutions. And I don't really think that the 15% is all that noticeable if you are detonating combos frequently. It is a simple additive power and weapon damage penalty, which does not affect ammo damage and I doubt affects combo damage. It really isn't a bad trade for a whole lot more shields.
I prefer the GPS for SP spam. For pure weapon, I would go Typhoon and either GPS, Venom, or maybe even Reegar.
Against Reapers specifically, you can try to throw down a Hex if there is a Ravager attempting to bombard you. Make sure you aren't standing too close to it or else sometimes you take damage anyway. For Banshees, if you are spamming SP, you can get her to put up her hand of denial when she stops hopping, which buys time to move away from her (if you are having issues). If you are running pure weapon, back away from her and keep firing.
Mainly pay attention to where the enemy units are, and where you can go to use right hand advantage to do damage. Think about where respawning units may come from, and think about where you may need to retreat to if too many units start to swarm you.
Collectors are probably a worse faction for the Jugg than the Reapers.