ToT LFR>ToT Normal>Timeless>SoO LFR>SoO Flex>SoO Normal>SoO Heroic
At this point in the expansion, new players and new alts alike get Timeless gear and from that starting point, all of ToT is ignored, even though ToT drops upgrades for the Timeless geared player. Instead, the focus is on getting into SoO LFR to get to SoO Flex to get to SoO Normal. This makes sense, of course. Why go through the hassle of a ToT Normal, with all the logistics involved, with varying gear/skill/experience levels likely present? Why do all that for ilevel 522 gear, old Tier sets and old trinkets, all of which are likely to be replaced by SoO 528 gear and current Tier sets and trinkets? Just as soon as you get to 496, you can start hitting the loot pinatas of SoO LFR and get newer, higher ilevel gear.
Except that higher ilevel isn't necessarily better. Newer Tier sets and trinkets aren't necessarily better. Also, choosing between SoO and everything else is a false dilemma. There are many options for gearing up.
The way I approach gearing up is by embracing the complexity and exploring options. First, I think this ordering of content itself is wrong, and very counterproductive. As such I arrange content by ilevel and add a few other sources of gear (world bosses excluded, as they are random):
JP Vendors, Timeless 489-496>ToT LFR 502>Heroic Scenario 516>Valor Vendors/Crafted 522>ToT Normal 522>SoO LFR 528>Timeless 535>ToT Heroic 535>SoO Flex 540>SoO Normal 553>SoO Heroic 566
And now for Adventures in Paint!
That would have been so much easier in AutoCAD, but I do not have that.
Anyway, what that graph shows is the relative distance between ilevels. There's 3 groupings that I will call A, B and C.
Group A gets a player out of leveling gear. It serves as a base from which to get gear from Group B. There are also a few pieces that are particularly strong for their ilevel, and should be considered even when gearing up for SoO-N
Group B is a mix of ToT, SoO, Valor, and crafted gear (I forgot to note the crafted, sorry, moving on). This is where the bulk of effort should go if SoO-N is the goal.
Group C is largely only available to people who are already raiding, unless they get lucky with world bosses, have enough gold for crafting, or have people who can carry them.
For illustration, I'll give the gearing up plan of action I'd recommend to a new Prot Pally, freshly dinged 90, in leveling/questing gear, and wanting to get into raiding SoO Normal ASAP
Gearing from Group A
Before anything else, get good trinkets, a weapon and a shield. There is one item I highly recommend getting, not for it's ilevel, but for it's performance. Lao Chin's Liquid Courage is very well itemized, compared even to ToT trinkets. It only costs JP to get, but don't waste VP upgrading it. To go with it there's: Relic of Niuzao, Alacrity of Xuen, Ghost Iron Dragonling, Iron Protector Talisman (463), Iron Protector Talisman (450). It's not the ilevel of any of these trinkets that keep you alive, just their performance. For a weapon, Maki's Mashing Mace, a quest reward from The Arena of Annihilation is good enough to run ToT LFR with, but you'll eventually want something better for SoO. For a shield, get Daylight Protectorate.
Get the quest Heroic Deeds and hope something nice drops from the Cache. Do the quest Path of the Last Emperor for Sabatons of the Humble. Then get as many Timeless items as possible, using Burdens of Eternity on off-set pieces, i.e. bracers, belt, boots, rings, neck. Prot Pally needs Tier gear in Tier slots, since having 4 pieces of 528 Tier gear is better than 4 pieces of 559 Warforged pieces (source). As such, 535 gear in those slots is inadvisable, as they could likely get replaced by 528 gear. Then go to the Justice Point vendors and fill in the gaps. Don't bother getting Vaporshield Medallion/Medallion of Mystifying Vapors, since even the 450 version of Iron Protector Talisman is better. If you have extra JP, buy it for the ilevel boost but use something better.
After getting Timeless gear, run ToT LFR. It makes capping Valor easy and gets rep with Shado-Pan Assault, which you'll want at friendly. You'll also likely get a better weapon and shield. If you get Fabled Feather of Ji-Kun or Ji-Kun's Rising Wind, they're third behind Lao Chin's and Relic in performance so far. If you get other 502 trinkets, just keep them in your bags for the ilevel boost. Mogu Runes are only 1,000 Timeless coins each, so getting a few and rolling on bosses that drop weapons (Jin'rok, Iron Qon) and shields (Primordius, Lei Shen) may be worth it.
Cap Valor every week, but don't spend it yet. Save it for better gear.
Gearing from Group B
Once at 496 ilevel, the goal is to get 4 piece Tier and good trinkets. Run SoO LFR and as much Flex as possible. Get Vial of Living Corruption, which is BIS at any ilevel. If you are hesitant about surviving SoO LFR at only a 496ish ilevel, run as Ret or Holy and put your loot spec as Prot or Ret, depending on what the boss drops. With a good weapon, shield, trinkets and some skill, though, you should be fine.
Heroic Scenarios can get the last bit of Valor you need per week, if you don't care to run ToT LFR anymore or do Timeless Isle quests. The gear you get is random, but if you like doing them, you can replace 496/502 gear with it.
ToT Normal or Heroic is an option, if you have the opportunity to get in a guild achievement run or a group on Open Raid or something. The advantage is that you'll likely be running with people who don't need the gear. The disadvantage is that, while it's not as random as Heroic Scenario gear, it's not much better either. It is an option, though. If nothing is dropping in SoO LFR, run ToT as well for more upgrade opportunities, even if you don't need the Valor.
Run Flex SoO as soon as you can get a group that will take you at whatever ilevel. You'll definitely want to down Garrosh for an heirloom, which will likely be a major upgrade. Also, you'll get more chances at gear every week, and practice with the mechanics of the fight on normal without as much difficulty. Spend a Warforged Seal on Malkorok as Prot until you get the Vial trinket, but also start saving up to 10 so that you can spend more on normal mode later.
Once you get close to capping Valor, spend enough every week to avoid capping, but save 2,000 for upgrading 553+ gear. The first slots to upgrade should be shield, trinkets, and Tier gear. Also, the Shado-Pan Assault vendor will allow you to replace any remaining 496/502 gear with 522, but only spend Valor there to avoid capping. An item of note, if you have been very unlucky with trinket drops, is Brutal Talisman of the Shado-Pan Assault.