Use C2. There are a lot of problems like that you'll run into in CC. Seriously, if it's it all possible, I'm not joking, using C2 will make things much, much easier.
Otherwise, what I generally do is have multiple layouts that are there only to store objects. To avoid a memory leak that happens when editing an object's animations sometimes, I split them up among multiple layouts so I don't have too many objects on any one layout. Then I restart construct after editing a few objects to edit some more, because I never know when that memory leak will happen. Keep in mind I have like 500 objects and thousands of animation frames though, so you might not encounter this bug.
When coding, to find objects quickly, upon creating a condition or action, type a few letters of the object's name and construct will filter the list, making those objects easier to find.
Any large static images I load at runtime with the sprite "load image from file" action, because large images add to the compile time significantly.
I've had several times where my .cap has got messed up. The only thing you can do about that is save new versions often. Very often. Like at least one per day. I generally do one or two new versions per day.
Depending how large your project is, there are miscellaneous bugs you might encounter. For example, don't use the layout object. Just don't. Even if it seems like it's working, it might not work in another layout with exactly the same code. Or, upon closing the layout object, construct might revert to using the wrong event sheet.
If you have a ton of events, it might bog down your computer as well. It currently takes about 7 seconds for my computer to acknowledge any edit I make on one particular event sheet. That's very unpleasant to work with. I could split up the events into multiple event sheets, but then it takes way longer to compile, and it's about 5 minutes to compile already.
That event sheet, by the way, takes 10 minutes to open before I can edit it. Even though it's approaching 6000 events, it still shouldn't take that long regardless because another event sheet with about 1500 events loads in a few seconds. I might not have the fastest computer in the world, but it shouldn't take that long to open.
Don't delete variables. Especially family variables.
When adding family variables, always use the family manager to do it. I heard the bugs involved in not doing it this way have been fixed, but I haven't been willing to try yet.
Basically, using construct two is a vastly superior experience. Not to mention the idea of reusing the framework I've created for any possible sequel is basically out of the question. Deleting an object - ONE object - locks up my computer for an entire half hour. It would take days - maybe even weeks to delete the stuff that the sequel wouldn't have!
More platforms, less bugs, better usability, more reusability. C2.