Yeah, 4E and Pathfinder both require some specific assumptions about encounter design. For example the same map in both systems can have two entirely different looking encounters. In Pathfinder, a couple of orcs makes a suitably challenging encounter. In 4E a couple of orcs isn't even an encounter - you need different terrain elevation, a few different orc stat blocks and maybe a piece of hazardous terrain (like a campfire) to make the encounter interesting. But some of the design principles will be exactly identical. In both cases many DMs respond better to a more "open" adventure, which lets the PCs decide where to go a bit more than a series of linear and heavily rail roaded encounters. Many of Paizo's AP adventures are great, but they can feel very on rails to achieve the deep storytelling and detail they provide. So striking a balance between giving a DM tools to run the adventure in different ways - while not trying to go overboard on producing material nobody uses - will be a difficult decision. Additionally in terms of differences you have to consider that Pathfinder has exponential power increases in casters - so later adventures need to consider balance very differently. That's somewhere I specifically won't be able to help much, because it's a long time since I DMed a 3.5 variant system, so building encounters around these issues isn't a strong point for me anymore.
While PCs in 4E become very powerful as well, my experience in paragon and epic games will certainly help out there should we get there - especially because the time we do it's likely my current two games will be in those tiers anyway! These tiers though can be designed wildly differently, because casters in 4E aren't quite as powerful and able to "bend" the rules so much. So many of the same design assumptions that make exciting heroic encounters can still be easily applied to paragon/epic tiers. A whirlpool hazard in heroic in 4E just becomes a torrent of elemental lightning and rain by epic tier. Same overall game effect (with better statistics), but more fitting the tiers theme and feel.
Edit: In terms of 4E, we should aim for an adventure more like the Slaying Stone (HS1) than Keep on the Shadowfell. HS1 was received a lot better by the community in general, as it was more open and felt like the PCs choices had more impact. Whereas something like Keep on the Shadowfell can feel like a linear series of endless combat encounters for 4 levels. I also feel limiting each "modules" levels from say 1st level to 3rd level is a good idea. Don't bite off too much and instead make them two quality levels - not just pad things out for the sake of getting 40 combats to get 4 levels into one module.