After some reading, wow is that Homonculous fragile as heck. It only gets trifling natural AC! My first guess would have been to use it like an animal companion, but it makes Wizards look robust! But it flies, gets simple weapon proficiency, and becomes Medium at 4th, and can use your extracts.
I'd play a Halfling and use it as a flying artillery platform. Have it use a sling or longspear and sling things myself. But even that is lackluster thanks to losing Throw Anything to no real gain, and Bombs. The real benefit of the Archetype would have been Craft Constructs, but that's gone.
Or I guess a mounted charger build and just avoid anything with greater reach.
Yeah, that's pretty much my reaction as well. The homunculus initially starts off okay, but as you level up, well....
If I compare it with a bipedal eidolon, and a horse animal companion (ignoring armour, evolutions, and magic items) then:
At level 1: a homunculus gets
15 Hit Points (5.5 per Hit Dice, and 10 for being a Small sized Construct) and has an Armour Class of
15 (+1 from size, +2 from dexterity, and +2 from Natural Armour), a bipedal eidolon has
6 Hit Points (5.5 per it Dice, and 1 from Constitution) and has an Armour Class of
13 (+0 from Medium size, +2 from Natural Armour, and +1 from Dexterity), and a horse has
13 ([4.5 per Hit Dice] times 2, and [2 from Constitution] times 2) with an Armour Class of
14 (-1 from Large size, +4 from Natural Armour, and +1 from Dexterity).
At level 5: a homunculus gets
47 Hit Points ([5.5 per Hit Dice] times 5, and 20 for being a Medium sized Construct) and has an Armour Class of
14 (+2 from dexterity, and +2 from Natural Armour), a bipedal eidolon has
32 Hit Points ([5.5 per it Dice] times 5, and [1 from Constitution] times 5) and has an Armour Class of
18 (+0 from Medium size, +6 from Natural Armour, and +2 from Dexterity), and a horse has
37 ([4.5 per Hit Dice] times 5, and [3 from Constitution] times 5) with an Armour Class of
17 (-1 from Large size, +6 from Natural Armour, and +2 from Dexterity).
At level 10: a homunculus gets
64 Hit Points ([5.5 per Hit Dice] times 8, and 20 for being a Medium sized Construct) and has an Armour Class of
15 (+3 from dexterity, and +2 from Natural Armour), a bipedal eidolon has
52 Hit Points ([5.5 per it Dice] times 8, and [1 from Constitution] times 8) and has an Armour Class of
23 (+0 from Medium size, +10 from Natural Armour, and +3 from Dexterity), and a horse has
60 ([4.5 per Hit Dice] times 8, and [3 from Constitution] times 8) with an Armour Class of
20 (-1 from Large size, +8 from Natural Armour, and +3 from Dexterity).
At level 15: a homunculus gets
86 Hit Points ([5.5 per Hit Dice] times 15, and 20 for being a Medium sized Construct) and has an Armour Class of
16 (+4 from dexterity, and +2 from Natural Armour), a bipedal eidolon has
78 Hit Points ([5.5 per it Dice] times 12, and [1 from Constitution] times 12) and has an Armour Class of
28 (+0 from Medium size, +14 from Natural Armour, and +4 from Dexterity), and a horse has
90 ([4.5 per Hit Dice] times 8, and [3 from Constitution] times 12) with an Armour Class of
23 (-1 from Large size, +10 from Natural Armour, and +4 from Dexterity).
At level 20: a homunculus gets
102 Hit Points ([5.5 per Hit Dice] times 12, and 20 for being a Medium sized Construct) and has an Armour Class of
17 (+5 from dexterity, and +2 from Natural Armour), a bipedal eidolon has
97 Hit Points ([5.5 per it Dice] times 15, and [1 from Constitution] times 15) and has an Armour Class of
33 (+0 from Medium size, +18 from Natural Armour, and +5 from Dexterity), and a horse has
120 ([4.5 per Hit Dice] times 16, and [3 from Constitution] times 16) with an Armour Class of
25 (-1 from Large size, +12 from Natural Armour, and +4 from Dexterity).
The homunculus, in comparison to the other two, is definitely weaker. It starts off with an initial Hit Point total above the other two, but it loses that advantage due to the bonus not scaling, and it's armour class is pathetic compared to the other two. The eidolon gets a whole bunch of evolution points in addition to it's respectable health and excellent armour, and all the classes with access to an animal companion also have access to ways to buff up their animal companion (meaning animal companion specific gear and spells, not general buffs).
Spell resistance at 11+ master's alchemist level is pretty good, as it adds up to almost 50% spell failure chance, and evasion/improved evasion help make up for the homunculi's shitty Reflex saving throw, but neither of those help stave off normal everyday damage, which is the biggest threat to the homunculus with it's shitty armour class and lack of access to healing.
It really seems to me like the homonculus is missing a few features.
Anyways, so far, the best options I can see for the homonculus (at least at level 1) are, as Keldar said, the longspear and sling, with bog standard leather armour, although I'm wondering whether it would be worth using up the precious feat slot for Light Armour Proficiency. Any ideas?