There are currently 249 weapons (including named and exotics as separate items), 23 brand sets, 13 gear sets, 44 named/exotic gear pieces, 41 skill variants, and 6 specialisation weapons. So that's 376 individual proficiencies to gain and 10 levels of each. That's obviously not counting any new items added in the new season.

First off, everything I talk about here is from the Intelligence Annex here: http://ubi.li/PFoYL so please refer back to that for anything you wish to confirm/clarify/contradict.

I'm starting this thread because I'm seeing quite a lot of misunderstandings about the new Expertise/Proficiency systems, and would like to try and clarify some of the less obvious points about how it is planned to function, and also some of the rather surprising ways in which it could affect our gear choices.

Explanations
First off, we need to look at the two interconnected systems of Proficiency and Expertise.
Proficiency is earned on a per-item-type basis, and affects which items can be improved. Proficiencies have exactly 10 levels each, which are earned by playing with the item(s) equipped, or by donating items and/or materials.
Expertise is earned on an account-wide basis, and affects how far items can be improved. The number of possible expertise levels is currently unknown.

For Proficiency, items are grouped by type as follows:

Weapons (Black Market AKM, P416, SOCOM Mk20 SSR, etc).
Brands (Gila Guard, Alps Summit Armament, Walker, Harris & Co., etc).
Gearsets (Striker’s Battlegear, Aces and Eights, Hunter's Fury, etc).
Named Items (Fox’s Prayer, The White Death, The Hollow Man, etc).
Exotics (Liberty, Diamondback, "Tardigrade" Armor System, etc).
Skill Variants (Explosive Sticky Bomb, Incinerator Turret, Defender Drone, etc).
Specialization Weapons (Survivalist Crossbow, K8-JetStream Flamethrower, P-017 Missile Launcher, etc).

By my count, this means there are currently 249 weapons (including named and exotics as separate items), 23 brand sets + improvised (probably treated as a single brand set), 13 gear sets, 44 named/exotic gear pieces, 41 skill variants, and 6 specialisation weapons. So that's 377 individual proficiencies to gain and 10 levels of each, giving a total of 3770 possible proficiency levels to gain. That's obviously not counting any new items added in the new season.

Now, proficiency levels go up to 10 for each item, and no item can be upgraded until its proficiency level has actually reached 10. As far as "which items can be improved" then, the individual proficiency levels are simply progress markers and offer no benefit until you reach 10. They do offer a benefit to your Expertise level, but we'll get to that later. It's also important to note that once a profiency has reached 10, it cannot be improved any further. This means that as soon as you can improve an item (even by only 1%), continuing to use that item will not increase the amount by which you can improve it! (Except by going down the donation route, explained later.)

Expertise controls how far you can improve eligible items, and is increased by gaining proficiency ranks for any proficiency. At this stage, we do not know how many proficiency ranks are required to gain a single expertise rank (very likely the devs want to do further testing before deciding on the best number), which means we do not know what the current maximum number of improvements you could apply to an item actually is.

Examples
For this reason, if one is focused primarily on improving items by use rather than by donation, we get the following results (for the sake of the example, I'm going to assume each expertise rank costs 100 proficiency ranks):

A standard high-end loadout likely has 10 different proficiency classes equipped (1 specialisation weapon, 3 regular weapons, 4 different brand set/named/exotic items (assuming 3pc of one brand or 2pc of two), and two skill variants.
By playing enough with this build equipped, one would therefore achieve max proficiency in 10 proficiencies, giving 100 proficiency points total towards your expertise. If that equals one expertise rank, you could then upgrade all 10 items/skills by 1%. However, continuing to play with these items will not increase your proficiencies any further, as they're all now max level. You could farm items & materials for donation and improve other proficiencies that way, but the proficiency xp you earn in that time by playing will all be wasted.

If you then equipped a completely different set (different items, skills & specialisation) you would lose that 1% bonus, but you could earn another 100 proficiency ranks - and once you're there, you can upgrade both your new loadout and your previous one by another 1%.

Perversely then, the fastest way to gain the most improvement in your gear is by always using items you can't improve yet, until you finally gain all proficiencies and can go back to your favourite loadout, suddenly gaining a huge power increase in the process. In practice of course, you'd be using donations to improve whatever items you least want to play with, and perhaps mixing your improved gear into your loadouts to help 'carry' the weaker, unimproved items. Rather than the usual 'Jack of all trades, master of none' setup, here we have to be jack of all trades before we can be a master of any of them!

Observations
One little piece of phrasing about leveling proficiencies through gameplay caught my eye:

Using the items in the field and getting kill XP with them

Note that it specifies kill XP here, presumably to exclude the 'activity complete' xp that makes up the vast majority of a players xp gains. I would guess that this is to prevent players exploiting the system by playing most of a mission/activity with their strong, upgraded gear then switching to an unleveled loadout to get the completion xp. However, this does raise the question of whether DPS builds in co-op will level their proficiencies far faster than support builds such as healers, tanks and CC?

The donations system will be great in finally giving us a use for all the junk we find (for longer-term players who have already maxed the builds they want, 99% of drops get ignored or trashed), however I'm thinking it will make exotics much more difficult to level up in this way, as their drops are far rarer. It'll also likely see an end to a lot of the exotic sharing that currently goes on, which will hit newer raiders especially hard (I suspect quite a large majority of people got their first Eagle Bearer/ Ravenous as a share from a more experienced raider!)

Suggestions
I would personally like to see a progression system for proficiencies beyond level 10, so we're not effectively penalised for using these items. Perhaps a traditional xp curve on subsequent levels (so each level takes longer to earn than the previous) to gain item-specific points instead of contributing to the global expertise level (points that could be spent on specific handling attributes or similar, like Keeners Watch). For exotics, it would be good if improvements could somehow be made to their talents (which is what makes them so unique and useful) instead of just base damage/armor.