Although my opponent predominately used sun our 3 battles which was unexpected when team building before our matches I immediately thought to abuse the lack of Ferrothorn.
When team building 3 pokemon that immediately came to mind in terms of offensive pressure were Zekrom, Latias and Kingdra.
Zekrom hates Ferrothorn with a Since its one of the few Pokemon that resist its dual STAB and being physically orientated Zekrom will take damage when attempting to break through, therefore it must run either the shaky Focus Blast or rely on team members to severely weaken or destroy Ferrothorn before it can be used to its full potential. Since even its Choice Band set is a 3 hit KO with Bolt Strike!
The Zekrom I used in one of my matches was a Tailwind variant with excellent wall breaking capabilities and it seemed the perfect candidate to unleash with Ferrothorn gone as it was then able to run Bolt Strike, Outrage and Draco Meteor with little fear of being walled. It was a tough choice between using this Zekrom and the Choice Banded variant, but the idea of making Zekrom difficult to revenge and able to outspeed even common scarfers was more appealing at the time.
As mentioned in the OP I was excited to utilise Latias as somewhat replacement for Ferrothorn in countering Kyogre and also the ability to set up Calm Minds and sweep with the same coverage as Zekrom in Thunder and Dragon pulse. Latias certainly did its job well since replacements for Ferrothorn that I was expecting like Skarmory certaintly couldn't stand up to it.
Then in my final team I attempted to run swift swim Kingdra as a potent revenge killer and sweeper. Like Zekrom and Palkia, Kingdra as greatly appreciates the removal of Ferrothorn, and since its also far weaker then the two aforementioned it doesn't stand a chance getting past it, So as a result its Mixed Attacking set whhc compromises of purely STAB becomes that much deadlier.
Although Kingdra didn't get to go the sweep I hoped it would (Curse you thunder wave Kyogre) its certaintly a force to be reckoned with.
Concerning defensive replacements for Ferrothorn, there isn't really a single one due to its unique attributes but Grass Arceus and Skarmory were certainly around to attempt to pick up the slack.
Again, as mentioned in the OP Ho-Oh does miss having Ferrothorn around to set up on but I did witness first hand a Ho-oh under the sun and cause me major problems since I relied on Grass Arceus and Latias to take on what I thought would be rain teams, leaving me entirely unprepared to combat sun teams without the rain in play, something which I'll be sure to rectify in round 2.
In terms of missing Ferrothorn, I can't really give any clear instances since like I said my opponent primarily used Sun which isn't a favourable match up for it in the first place, but i remember missing having a Pokemon able to switch in and be able to take strong dragon moves. Since at that time I was using a team which simply had Ferrothorn subbed out in favour of support Dialga which could not stand up take Modest Reshiram's Draco Meteors for long, and since the Reshiram was also scarfed I'n sure my opponent realised that he could simply spam Draco Meteor when it was in safely without drawbacks. Although that was poor teambuilding on my part, since I should have changed it to Support Arceus-Steel or Chansey rather than Dialga.