Some random thoughts based upon 20+ years of Orlando vacations and my dd working as a CM at Disney:
1. Two weeks is an awfully long time for a 6 year old and a 1 year old to be away from home, in a small hotel room. It's also not necessary to spend that long to see what kids those ages want to see. I'd cut it back to 10 days max, probably closer to 7.
2. Kids often surprise parents with their preferences. Example: kids are often just as thrilled to go swimming than they are to go on rides. So make sure your hotel has a good pool and you bring swimsuits and PLAN for swimming (and also the need to take decompression breaks because the parks are often overstimulating for children). Another example: I thought my then 6 year old dd would be thrilled to have the Princess breakfast in Cinderella's castle. It was fine for her, but what she really loved was Hoop De Doo -- she talked about that for months after! So carefully consider what your kid will really enjoy.
3. I'd skip Epcot and possibly Hollywood Studios at Disney. We love Epcot, but with a very few exceptions, most kids are not fans of it. Toy Story Mania at HS is the hottest "ticket" at WDW because it's really the only kid-friendly ride in the entire park. Riding it generally means you must get there at rope drop and hustle right over there to get in and/or get a FP for later. Don't hustle? On an average day, you won't get a FP and you'll have a 60 minute wait. So with kids of that age, you need to ask if it's worth it.
4. The best way to get the most done with the shortest lines is to get to the parks at "rope drop" -- which is as soon as it opens. By doing so, you will be able to get on rides while waiting the shortest possible time, which allows you to get on more rides before the kids get tired and/or the parks get crowded. If you do not get there for rope drop, plan accordingly and understand that you WILL have to wait on lines, sometimes long lines. Prepare everyone for that reality.
5. Understand how to use the FP system at WDW and how it differs from the systems at Universal and Seaworld.
6. Get on Disney, Universal and Seaworld's email lists. Disney will send you regular offers of discounts and free dining options that are worth using. Also, if you belong to AAA -- they often have great deals. For example, this year they had a deal so that if you bought a Seaworld one day pass, it became an annual pass.
7. If you are planning on going to SeaWorld and Universal, you'd be better off renting a car or staying at a hotel with shuttles to those parks because the cab fare to get from, for example, Disney's Pop Century Hotel to Universal was $40 each way. That's $80 per day in cab fare that would have covered most of a week's worth of a car rental.
8. We have stayed at a variety of Disney hotels and off-Disney hotels. Our favorite Disney hotel with kids is Pop Century. It's a value resort and has a good cafeteria right on site, as well as numerous pools. Another huge advantage is that the Disney bus service for Pop is only for Pop, unlike many other resort buses, which are shared. We do not find any value to spending a lot more money to stay at the moderate Disney resorts such as Port Orleans. We have also stayed at the Holiday Inn Express in Buena Vista and the Holiday Inn Resort in Buena Vista -- both fine (and the Holiday Inn Resort has an option for a very large room at no additional charge at times, which is a god send if you have a pack and play and a car seat, etc.) I'd also note that if you sign up for Groupon, they often have Disney area hotels on sale. In fact, just today, they had a deal for a Disney-partner hotel for only $57/night.