Which update was that and what did it do to it particularly? I'm getting that gun pretty soon, so I would like to know.

1 word: Wow.

The Iron Slug is not all sunshine and roses.

I was mentioning the differences between old Iron Slug and new Iron Slug, which is phenomenal.

2. All 2-shot weapons suffer for being...2 shot weapons. Lots of reloading. PITA for breaking 3-hit blocks.

You have two weapon slots for a reason. I'm pretty sure there aren't that many people out there who are a dead-center hybrid running heavy weapons like me, maining Sudaruska (2-hit), Iron Slug (2-hit) and a Bomb (Charge only)

3. The charged shot is stopped dead cold by anything with a shield. You can't fire through Mecha Knights to get to the Gremlin Mender behind them.

All weapons are stopped dead cold by anything with a shield. This is nothing new.
If you need to injure enemies with shields you shoot on an angle so that you can graze their back

4. The "Knocked back based on the direction they are facing" thing is a real nuisance. I have to think it's a bug, but it doesn't seem like one OOO is in any great hurry to fix.

How is it a nuisance? It's extremely useful for pulling wall-hugging zombies out of corners, pulling attacking mobs away from teammates, and in general creating paths through mobs that are blocking your way with their tightly-packed bodies.
If you have aggro of the mob that you're attacking, it makes no difference as they'll get knocked away from you anyway.

5. Even with max charge time, the charge time is pretty slow.

All guns (with the exception of the Catalyzer line) charge at the same speed, that includes the Iron Slug:
http://wiki.spiralknights.com/Magnus#Charge_Attack
http://wiki.spiralknights.com/Blaster#Charge_Attack
http://wiki.spiralknights.com/Cryotech_Alchemer#Charge_Attack
http://wiki.spiralknights.com/Autogun#Charge_Attack
http://wiki.spiralknights.com/Pulsar#Charge_Attack

6. Lots of movement pauses for regular shots and charged shots and reloading. You have to be very careful that these stops don't get you whumped by something.

This is the same for the Autogun line, another weapon highly appraised for its massive damage output due to its brilliant charge, (FYI reloading doesn't incur a noticable penalty on movement speed) as well as all other "Heavy Weapons", i.e. Troika, Sealed Sword and Rocket Hammer. It's an occupational hazard :)

8. Bad for Puppies/Howlizters/Polyps unless you can arrange for the range to be exactly right so the flight terminates right on top of the turret. If you can do that, it will generally one-shot the turret, otherwise it only hits once and passes through for pretty poor damage.

You're forgetting about the really high chance of stun (no other gun inflicts stun :3) on the charge, as well as the garunteed flinch. Since turrets are the only mobs to attack constantly regardless of range, target, or facing, stun affects their offensive output more than any other mob. Two shots from an Iron Slug in larger parties will also garuntee a flinch, and if you practice the timing, you can flinch-lock them indefinitely. Stun makes the flinch-locking even easier by increasing the window of attack. Flinch-locking enemies is incredibly useful when facing Rocket Puppies as well as Gremlins, especially the peskier variants (Menders, Demos, Ghostmanes and Mortifires)
The best thing about Iron Slug regular shot induced flinching is that it doesn't cause knockback like pretty much every other flinching weapon, (bar the non-pepperbox Autoguns and the DBB) allowing your teammate to easily finish off the immobilized mob.

>I was mentioning the differences between old Iron Slug and new Iron Slug, which is phenomenal.

Old versus new is certainly a huge improvement, but no weapon is perfect, and the Iron Slug comes with drawbacks.

>How is it a nuisance?

Not every monster is so obliging as to face you. I'm less interested in getting them out of corners or pushed in random directions than getting them dead. Gremlin Menders are particularly annoying in getting them to face the right direction to kill them.

I agree with the iron slug

And about menders and any enemy, just walk in front if them, its that easy, and if you're actually focusing on it the iron slug would have already drawn its aggro if not killed it already

And about turrets, if you hit in the middle if the charge, you get 2 or 3 hits, and its not as hard as you make it out to be hitting the end of the charge

The only thing I can think of for you not getting that many hits in would maybe be lag, its not uncommon for SK to decide not to show you some things, a few times I've noticed in dreams and nightmares I use an iron slug charge and the damage numbers don't show, because the only time I ever get single hits is if I shoot an enemy's side, back, or the absolute tip of the charge

winter grave.game over.

Get a Punch or Pummel gun. These functioned just like the magnus line before the update. In the update the Magnus got changed but the Punch/Pummel guns stayed the same.

I'm not sure if they still knock you down but they don't get multi-hits like the magnus does now.

Personally I think the Valiance is the best gun. It has no downsides and is incredibly easy to use and effective in any situation.

As Sir-Zeddybear said above, the Volcanic Pepperbox also deserves an honorable mention, being one of the extremely few decent normal damage weapons before the Gunner update (along with Nitronome, Sudaruska and Valiance)
The charge's knockback has its uses (both before and after it was "fixed") as well as being able to one-shot most mobs (especially all turrets)
The Volcanic Pepperbox is also the only weapon that was, and still is exceptionally effective against all bosses (in addition to being the only weapon apart from Divine Avenger to my understanding that could one-shot RT phases, until the Gunner Update which added Slug, Grave, AP and Sentenza to that list)

EDITED to reflect people's mentions of other stuff that destroys RT

I've pulled off phase enders with the Twins using the 4 star Avenger, but it's very inconsistent, even with a medium construct UV. Since I found the Slug could do it faultlessly, my Avenger has been gathering dust.

Go back to your porridge-eating bears, footwear residing grandparents and canines who can talk and be mistaken for people when they wear old people's clothes, because we all know that the mixmaster isn't real

I love my battle bears.

Anyways
http://imgur.com/9M4x6e5

Nice photoshop buddy