What is your preference with apps? Would you rather use Native apps or 3rd Party apps.
Personally I think they both have their place depending on what you want to do and at times you have no choice but to go to a 3rd party app. I try to use Native apps whenever I can myself.
Thing of it as a general vs specialized. Apple apps are general; they provide basic set of features, because Apple needs to distribute their resources evenly to work on iOS as a whole.
3rd party software is specialized. They concentrate on one thing, and they try to do it better.
I use 3rd party where it makes sense, i.e. where I need more than what Apple has to offer.
E.g. time management (calendar / reminders). Apple omitted a major feature by not showing due reminders in calendar view. I need to see what my commitments are for the day, and I don't want to switch between two different programs for this. So I get a 3rd party soft - there's a number of great solutions (PI, Calengoo, free Jorte). I went with Calengoo because this is what I used on Android and I am used to the way it works. This doesn't mean that iCal or Reminders are bad - just that they are insufficient for my needs.
Same with Notes. If all needed was to type a quick two liner, it would be fine. But if I want to take meeting notes with some structure, do a quick sketch, or quickly hand write something, Notes is inadequate. Again, there's a number of solutions - Evernote, Springpad, a word processor like Pages, I settled for Good Notes - they allow handwriting, typing, even great for mindmapping, and it's a fast program.
I am using Google Hangouts instead of FaceTime. The biggest advantage is that with it I can call a US phone number on Wifi from my tablet using Google Voice for free. As far as I can tell, the video conferencing is about the same (not sure though if FaceTime allows video calling more than one person at a time like Hangouts does ? We often have 3-way video calls with other family members)
I don't have an iPhone, if I did I would likely use Waze for navigation. I have it on Android, and I find it better, especially for long distance travel, than Google maps - it has real time updates when there are major accidents or other delays along the way, while Google Maps is often late in reporting delays. I assume Maps on iOS would also be behind in the real time data.
OTOH, Safari is a good browser, and there's no reason for me to switch. Numbers is a nice, if bloated, program, and I could use it for a quick spreadsheet I don't intend on sharing.
Basically, you find the best tool that works for you, and depending on how much you use something, you may be ok with a basic version included with OS, or you may need a more specialized program to better suit your particular needs.