-------ABILITIES-------
Magnet is absolutely useless as a 2 energy cost ability.
There is a very limited amount of towers it affects (practically 5 towers), it doesn't scale from your peak damage, and there aren't any real single target threats it could be used on.
It should probably cost 1 energy. That would at least make it at least a consideration as a coin generator.

Another overpriced/underused ability is Windstorm. There is no real reason why an enemy can be affected by Windstorm(s) only once, instead of up to 3 times, and with buffs to Blizzard it might not even be as good at stalling enemies despite costing more. Blizzard itself, on the other hand, is doing great now.
Windstorm buff in 1.9 promotes its use for defense instead of stalling, but at 3 energy it cannot compete with Fire Storm, or Smoke Bomb. It relies on enemies having gained no knockback immunity, and doesn't actually provide significant defending advantage. The towers that could take advantage of enemy stacking are very limited in count and ability to actually get value from stacked enemies.

Another pair of questionable abilities, Bullet Wall and LOIC. It is a bit silly to have 2 abilities heavily favouring vertical maps in a game that is locked to horizontal orientation. And while LOIC has great damage potential at least, Bullet Wall really can't offer much nor can it be fixed with a number change.
LOIC buff in 1.9 doesn't really do much - economy is most important in earlier stages of the game, while the main point of LOIC is incredible damage potential, far surpassing any other ability, but very awkward to use.
Bullet Wall buff needs more testing. There probably will be levels where it is used regardless.

------------------TOWERS-----------------------
Cannon still feels terrible.
Missile might be decent - it definitely feels better to use now.
Flamethrower is very awkward now, it is really hard to make it spread the fire debuff because it doesn't switch targets like Venom, but forcing it leads to no enemies with the debuff instead. Solution - make it it constantly search for enemies that are not on fire, unless Cold Fire is selected.
Venom with Fast Shells (third ability) can act as a single target DPS tower, but it still wants to do AoE and poison everything, which is counterproductive.
Considering the bonus system, Sniper is still very strong. All of its abilities are now very efficient, so it goes out of control with "the bonus". The easiest change I could see is a nerf to Killshot, maybe? That way it will only be weaker on higher levels.
Personally, I would also improve explosion piercing by 5% globally, just to see if that is too gamebreaking. So far, it doesn't seem it would be problematic.

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Sniper got buffed quite significantly in 1.9 despite being the best spammable DPS tower in 1.8
Chart: https://www.desmos.com/calculator/yucf1d27np
This is without considering 1.1x damage pwrfactor that was also added in 1.9, which is yet another significant buff. As for abilities, very minor nerfs to Killshot and Ultimate, not enough to offset the buffs in 1.9, yet alone nerf the tower from being the best option is every gameplay mode (No research (DQ), Max normal, Max endless)

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Sniper DPS chart in image format attached

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Another correction - Sniper 1.8->1.9 is a 22.5% DPS buff, I added an extra 100% crit damage to both version on accident (which favoured 1.8). Updated chart - https://www.desmos.com/calculator/0tjpk55wth

Moving to next problematic point - Cannon Ultimate got nerfed: 400% -> 345% damage, which makes it deal less damage than Powerful (when it has x1.15 PWR to be specific) even if mines are always placed down and Cannon never misses a mine drop: Max Normal - Mines are 23.75% extra dps vs PWRful 32.25%. There is an argument to be made that mines have upsides that make up for this shortcoming, like being able to stack damage before a wave, but there are also downsides like short range and inconsistent/uncontrolled placement which would make it justified for mines to be as strong numbers-wise as the upgraded Powerful, its direct competition.
But most importantly, it is a nerf to a notoriously bad ability for a tower that didn't perform well, and seems like it still underperforms in Beta.

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A tower that fills a similar role to Sniper is Minigun, (Single Target Damage Dealers / Cleaup). From 1.8 to 1.9 Minigun saw a Damage Decrease of around 46% at each level of upgrade. This is on top of other changes such as the Minigun bullet spread and the slight nerf to its debuff. In 1.8, it was used to clean up enemies like Healer and Armored, but with 1.9 Sniper feels like a much better tower for dealing with these enemies despite having 50% less efficiency against said enemies. The minigun ultimate change was nice, however, powerful still out DPS' it on normal mode, even with both microguns dealing damage.

TL:DR
Sniper's Buff and Minigun's nerf effectively replaced Minigun's role against Healers and Armored. On normal mode, Minigun's ult (on paper) does not out damage powerful (making the ability feel kind of useless).