If everyone is taking the same penalties on combat roles, what does that do to effect the outcome?

The same penalties does not equal the same effect. Well, unless all the die pools are the same size.

If your character reduces the oppositions chance to hit from (an arbitrary) 25% to 10%, if you'll forgive me the clumsy math, you roughly double your characters chances of survival.

If at the same time you reduce your characters chance of scoring a hit from roughly 100% down to 85%, some would call that a good trade.

Your character misses roughly 1 in 5 shots for a doubled chance of survival.

Then again, your character used to put on armor to prevent damage....

yes, but everyone is missing what I am saying ... if all parties have their chances of success reduced by the same amount the overall effect is just shifting the whole range to the left. The difference in chances of success are the same so if you had a compared chance of success (for the encounter not individual action) of 75% (difference of 100 and 25) in scenario A, you also have then you still have a 75% (difference of 85 and 10) chance of success in scenario B. The only difference in A you can win in 2 or 3 actions while in B it takes you 5 or 6 actions

NOTE: yes this is using quick clumsy math but if you take them time to actually plot a probability curve you would see the same effect, and yes we went through several iterations of that study when developing the new system

Once again, chances of success do not equal the same effect.

Combat capable characters are generally built around 1 successful shot, one kill. It varies of course.

PCs typically (in the games I play in) take 3, maybe 4 successful hits before being taken out. Again, there is variation.

In scenario A, your character likely takes a hit.

In scenario B, your character likely doesn't take a hit.

Of course, that explains why 6e reportedly has increased the amount of healing available....