So, I was looking over the Phantom Thief and thinking "this is new levels of awfully bad". But is it really? Let's do a comparison.
At level 1, the Phantom Thief has a few class skills the Investigator lacks - Handle Animal, Ride and Survival; +0 to one of them, because the half level bonus doesn't have the usual "minimum one" clause; 2 more skill points; and finesse training (because unchained rogue is the only rogue).
The Investigator, meanwhile, has good Will saves, Inspiration (including free inspiration on all knowledge checks), Trapfinding and Alchemy.
At level 1, the Investigator seems to be the better skill user. Both of them look like terrible fighters, but the Phantom Thief seems slightly better at making melee attacks for 1d6 damage with his d8 HD and light armor proficiency. Advantage: investigator.
At level 4, the P.T. has 8 extra skill points (48 vs. 40 assuming +4 per level), Evasion, Uncanny Dodge, dex-to-damage with a melee weapon of her choice, Social Sense +1, 2 rogue talents with expanded options, and 2 skills with a +2 bonus and the level 5 unlock. Those expanded talent options are mostly "combat feat or skill focus", though. He can take Vigilante social talents, except for the one social talent that isn't completely terrible.
The investigator has Poison Lore, Swift Alchemy, Posion Resistance, can make untrained knowledge checks and has Trap Sense +1, all of which are trash abilities that he should really trade out by archetype. He also has a talent, Studied Combat +2/+2, Studied Strike +1d6, and 2. level extracts.
At this point, the Investigator can be a competent combat character; the PT is a medium-BAB character with no accuracy or damage boosts. To be fair, if both characters spec skills-only, the PT will be less terrible than the investigator at combat.
If we're speccing for skills, the PT takes skill focus twice because his other skill-boosting options are terrible, and the investigator takes Expanded Inspiration or Underworld Inspiration. PT gains +5 to two skills (and teeny tiny circumstance bonuses from skill unlocks), Investigator gains +1d6 to a total of 7 skills plus all 10 knowledges, with the option to spend inspiration on any other skill. For any specific challenge, the Investigator can completely blow away the PT with extracts.
Normally I'd do level 6, but apparently level 7 is good for the PT.
At this point he has 98 skill points vs. 84 (assuming +6/level), his skill buffs are 4 skills at +3 with level 10 unlocks, he has 3 talents total, and Social Sense is at +2.
Notable skill unlocks: Stealth abilities he could have had as racial traits at level 1, Bluff: if your GM wants you to succeed you can keep rolling, Diplomacy you can change attitutes in 1 round except not in combat, Disable Device you can disarm that once-in-a-lifetime magical trap at -10, Disguise you're almost as good as a 1st level extract, Intimidate is actually useful if you focus on it, Perception: the distance modifier (which your GM is totally applying by-the-book all the time) is reduced to one-third, Sense Motive: you can duplicate a 2. level extract with about the same odds of succes (if you take Skill Focus), except only the social intel-gathering ability, not the awesome tactical recon ability.
The investigator has 3 talents as well, his combat buff is +2/+2/+2d6, and he has access to flight and other tricks that the PT just can't duplicate.
I guess the Phantom Thief is for those times when you've made an in-character decision to kinda suck and you want your stats to reflect that.