Okay, my updated thoughts on the map, now that I've had the chance to play it with the new changes.
The spawn times seem a bit long, first off. I'd recommend decreasing them by about 3-5 seconds. The capture boxes seem too large to me. They really shouldn't extend that far beyond the cap point circle, in my opinion.
And lastly, the new capture point order. Now, I'm all for the map not being confusing to new people. However, whether it's linear or not, it's still big and confusing. Even though the points may be linear in capture order, the layout isn't so much. I still found myself running into closed doors at L and C several times, even with already knowing the map layout. With a map as large as this, exploring and learning it is going to be easier when you're not getting stopped by barriers half the time.
Basically, I had more fun playing it with the old cap order. I do like the addition of all the health and ammo packs, though. I also think that the fan above L/C should be removed. Maybe that's just a personal gripe, but I hate forgetting about it every time I try to rocket jump up to the ledge and end up suffering nearly 30 seconds of downtime for it.