Are the ideas people had about hacking things out of our techniques collated somewhere? It's trivial to come up with feasible ideas I don't recall being mentioned in the story, but I really don't want to trawl through hundreds of pages to stop myself saying something that's been "invented" a dozen times, or that got dismissed ages ago.
People were wanting a telescope earlier. Did anyone consider just making one from ice? Assuming basic knowledge of how telescopes work, which seems fair given that they exist, building an ice one seems fairly easy, if not quick. A storage seal plus temperature control means it can last, and Elemental Mastery's fine temperature control plus Vampiric Dew's water control are basically perfect for making clear ice.
How does overlapping Elemental Mastery work? If one used a -X° Elemental Mastery with a range of 10 metres, and followed with a +X° Elemental Mastery in a 5 meter range, what would the result be? What if two people were doing these simultaneously? Does the effect go through walls?
The mistinator ain't bad, but it's slow. It seems like boiling water with a bunch of explosion seals in a suitably contained vessel would be faster. The explosion sounds can be dampened by applying both Banshees locally and Silence Mines to quiet the escaping steam.
The boiling steam could be reduced to a reasonable temperature by using Elemental Mastery, which has the advantage of converting steam into mist fairly directly, as well as effectively containing around the mist in the local area because hot air doesn't carry water as well. The hot steam outside is a minor nuisance to opponents, especially harming their eyes and thus vision, and the mist is useful of its own. This can also be used to hide our sky-platforms inside of artificially created semi-clouds, though that's also a tell if used inappropriately.
How about using Vacuum Step as a projectile, assuming sufficient armor (spiky? seal-enhanced?) to make it generally more damaging for the opponent than the user? Risky, but powerful in a cinch. A sword or spear would be safer, if you have the fidelity to "stop" with just the blade in the opponent.
Why haven't we made a gun/cannon? It'd be easy and potent. Use a Five Seal Barrier on a tube with a flat surface at the end. Include a small cannonball and hook some internal explosive seals up to tripwires. You can't aim them, but a dense array of flak cannons (which can all be carved into the same wall) seems effectively undodgeable, and at least an order of magnitude more damaging than a pure explosive blast. Heck, the guns can even be mounted in the air, which to most ninja is probably somewhat unexpected. Obviously you Banshee Slayer the heck out of them, because hundreds of sniper flak cannons is basically an instant win condition.
Have people considered using Force Walls as near-invisible blade traps? Lay them flat over a path at waist height; an unsuspecting ninja running along that path gets neatly sliced in two, or at least significantly wounded if not running at full-pelt. If this can be tripwired, it's even easier to goad someone into the trap. The advantage here is that it's a silent trap, which makes it useful when stealth is a priority.
Banshee the hell out of your shoes. Heck, anything on you that can as much as crinkle gets a Banshee seal, as long as Kagome thinks it's OK. If a kunai's "whooosh" through the air is a useful tell for dodging them, Banshee them too.
Zephyr's Reach seems underutilized in combat, though I might not have been paying enough attention to the story to see what the restrictions are, or when it is used. I suppose it depends on its speed, but playing seals behind your opponent means your opponent now needs to fight in 3D, which hurts their attention, and if you're lucky you can wrap them in ninja wire. That's not a win condition, but even minor mobility impediments matter a lot in combat.
Kawarimi gives you the velocity of the object you swapped with. This sounds like great escape material; shoot the kawarimi target out of a horizontal cannon and swap with it. You are now really darn fast. Sadly it's probably not a good idea because of how finicky and dangerous it is, but it might be better than getting skewered.
Someone else mentioned underwater bases before I had the chance to post this. You can fix a large open-bottomed box in place, and then you're basically impossible to attack directly without the opponent getting in the water or using special jutsu. This won't work amazingly for long-term defense, since it's easy to trap you there, but for short-term protection it seems fairly solid. The idealized situational awareness and immunity from seals in the vicinity are huge bonuses.
A floating island sounds like a less traumatizing long-term base, as long as it's far enough in the water that it's not easily visible. Since the terrain is entirely flat, this allows you both to pepper the sea with a grid of kawamiri targets (on other platforms) and makes you extremely hard to sneak up on. Ice telescopes make the "you can't sneak up on us" point twice as true. Float the platforms at a jump's height above the water, with entrances you can close with MEW, to make attacks significantly harder.
The biggest problem is that you'd get lonely really damn fast. But at least you have Banshee seals to ignore the complaints with.