[RPG] penalty for “reaching into melee”

Soft Cover

Soft cover is cover, except with the differences that it says. Emphasis mine:

Creatures, even your enemies, can provide you with cover against ranged attacks, giving you a +4 bonus to AC. However, such soft cover provides no bonus on Reflex saves, nor does soft cover allow you to make a Hide check.

That's pretty clear. It says flat out that it provides cover against ranged attacks, with the exceptions listed. AoO's are not listed as an exception, so the Cover rules apply.

AoO's Are Blocked

From the cover rules:

To determine whether your target has cover from your ranged attack, choose a corner of your square. If any line from this corner to any corner of the target’s square passes through a square or border that blocks line of effect or provides cover, or through a square occupied by a creature, the target has cover (+4 to AC).

Here's your example:

C <-> F1 <-> F2

Assuming those are all medium creatures, there is no line between C and F2 that doesn't go through F1's square, so cover applies.

When making a melee attack against an adjacent target, your target has cover if any line from your square to the target’s square goes through a wall (including a low wall). When making a melee attack against a target that isn’t adjacent to you (such as with a reach weapon), use the rules for determining cover from ranged attacks.

This says we use the ranged rules for a reach attack, so it has cover.

You can’t execute an attack of opportunity against an opponent with cover relative to you.

Since it has cover, we can't do an AoO.

But! Large Creatures

Now consider this scenario:

---------            1234 = large creature
-12FG----            F & G = medium creatures
-34------
---------

Same thing as before, they're adjacent. Except C is now large. The rules say that a large creature gets to pick one of its squares to determine cover.

To determine whether your target has cover from your ranged attack, choose a corner of your square.

It can use #4 (as it can use any of its squares), and from that square it has the ability to hit G without going through F's square. As a result, G no longer has cover and the large creature can make an AoO.

That's also mentioned in the cover rules:

Any creature with a space larger than 5 feet (1 square) determines cover against melee attacks slightly differently than smaller creatures do. Such a creature can choose any square that it occupies to determine if an opponent has cover against its melee attacks. Similarly, when making a melee attack against such a creature, you can pick any of the squares it occupies to determine if it has cover against you.

On the upside, if G has reach, it can choose #4 as it's square as well, and it can attack the large creature without F being cover.

Yes, ranged attacks from spells are typically considered to be "weapon-like". This is definitely true of rays (and almost all ranged touch attack spells are rays) since from the rules:

You aim a ray as if using a ranged weapon

The rules further clarify that rays function as weapons for several other purposes, and the FAQ makes this very explicit:

Do rays count as weapons for the purpose of spells and effects that affect weapons?

Yes [...] rays are treated as weapons, whether they're from spells, a monster ability, a class ability, or some other source

The same rule applies to weapon-like spells such as flame blade, mage's sword, and spiritual weapon--effects that affect weapons work on these spells.

Most ranged touch attacks which aren't rays are things like acid splash -- spells where you actually throw or aim a physical object. Those are even more "weapon-like" than rays, so it's probably simplest to say all ranged touch attacks work like this.

There's another FAQ that indicates you can take "Weapon Focus (ray)" and the like; strictly speaking I guess those wouldn't apply to orb spells like acid splash.

This is all following the precedent set by 3.5; in Complete Arcane it specifies that rays and touch attack spells are "weapon-like" and thus interact with feats in the same way that other weapons do, with a split between ranged/melee type spells.