For example, let's pretend that +1 atk with sword, +1 atk with bow, +2 dmg with sword, and +2 dmg with bow are all perfectly equal feats. The moment I take +1 atk with sword, the +2 dmg with sword feat is now more powerful than either bow feat because of my previous choices--I plan to use the sword for a lot of my actions, so sword feats are now more powerful.
Let me take a different approach to this.
Ok, let's pretend let's pretend that +1 atk with sword, +1 atk with bow, +2 dmg with sword, and +2 dmg with bow are all perfectly equal feats. Now let's pretend that there is a fifth feat which says, "All of your feats that apply to swords, now apply to bows as well". Now, is this feat better or worse than +2 dmg with a bow? On the one hand, its clearly better, because provided I have '+1 atk with sword' and '+2 dmg with sword', then 'Bows are the new swords' is equal to two feats for the price of one ('+1 atk with swords' and '+2 dmg with swords').
But really, so what? We aren't trying to balance feats with each other. We are trying to balance the collection of feats available at a given level with a similar collection of feats. What were are interested in is, "Is three feats to get +1 to atk and +2 to damage with both bows and swords, attractive compared to any other three feats we might choose?" We don't really have to worry about the fact that many of our combinations are suboptimal at some level. We more have to worry about that there is no one, or few, set of choices. We can assume, and indeed even intend, for feats to be chosen in a synergistic way. So long as we control the synergy, we ought to be ok.
As you can see from the "Bows are the new swords", we can actually take advantage of this to discourage the sort of linear specialization you are worried about. With feats like "Bows are the new swords" when you have a choice of a third feat, you are now choosing between say, "improve +2 to atk with swords" or "improve to +1 to atk, and +2 to damage with bows". This is now a more legitimate tradeoff between depth and breath of skill than the third feat "improve to +1 to atk with bows" would be.
So yes, a badly designed feat tree never tempts you but to go deeper. But my preference in design is to push players less toward, "Design toward what you can kill", but toward, "Design toward what can kill you." The former encourages you to be a Johnny-One-Shot that can take down anything quickly. The later however encourages you to start at some point plugging up holes in your capabilities so that you are never completely outmatched or lacking answers.
If you have dozens of little variances between feats, I suspect you'll quickly find choice-fatigue paralyzes most players. They'll resolve their paralysis by growing indifferent, which would be a shame because it looks like you have a great template set out to provide a lot of choice and customization.
This is not my experience. I grant you that some players, especially casual players, will experience choice fatigue. In my opinion that group is smaller than the group that likes freedom to choose their own path and destiny. But yeah, for groups with wildly different tastes, you'd need wildly different systems to please them.