How would you decide between MOS 25D and MOS 25E?

25D class is really hard but it would pay off in the long run. They end up getting stationed at the NSA after AIT. 25E is no cake walk either and is a great MOS that still has bonuses but you can end up in a S3 shop and nobody likes the 3 shop.

Cyber defender...much cooler job title

Go Delta. I went from 27D Paralegal (Enlisted) > Signal Corps (Officer) > FA53 Automations (Officer) > 17A Cyber Warfare (Officer). Cyber is the future and will pay off in the long run. From 25D (Defense), get multiple certs and then go 17C (Attack).

Bottom line what interests you more? Delta is very difficult, it you want a taste look into attending CEH (certified ethical hacker) training offered by Global Knowledge. It certainly helped me decide against it but you may have a different experience. Echo is a great choice for 25U's as it used to be the natural career progression step for us. As SFC and above would transition to that status before it became a MOS of it's own.
Bottom line is what are your interests, do you like getting into the deep nitty gritty of computers? Have you worked in depth with Routers and Servers? What are your current CompTIA certs?

25D has more civilian application, information security continues to be a great area for development.

For 25D you would need to be promotable, an ALC graduate, and have 8 years TIS along with the other requirements for certifications and IT experience. If you meet that criteria I would suggest you go 25D over 25E. The skills and experience you will gain will directly transfer to the civilian world after you get out.

You should elaborate what you mean by "downfalls". What have you discovered that has you concerned?

As to the jobs and their pros and cons, a lot of that will depend on your experience and what you're trying to achieve.

Of the two, 25D is growing faster and is "the hot new thing" right now. Cyber attacks are quickly becoming a DOD priority. But Cyber Security isn't just a military concern. Fortune 500 companies are quickly recruiting the best experts they can find to harden their systems and mitigate risk. And I can say one thing with certainty: Cyber attacks are not going away. Look at Sony, Target, OPM, and countless others in the last year.

Of course with all of this in mind, cyber defense training is not trivial. It is technical, it is detailed, and it is constantly changing with every new attack developed and new technology invented. Just like medical doctors must constantly stay ahead of research to apply their knowledge and stay relevant, cyber defenders must do the same to effectively protect their networks. This is why our core training material for the military is not taught by military instructors but by civilian ones. They have the experience and latest tools that few others have. So if dumping TCP packets, reading hex, and working with complex command line syntaxes sound like your cup of tea, then you might make an effective 25D.

And the opportunities for a 25D post military are pretty nice. Our civilian instructors are proof of that.

which will help you get the job you want when you get out?

Do you like computers or radios better? Ask yourself that

I would say go for what you feel you could best serve the country through. Don't pursue any MOS or assignment in the Army that you feel will "give" you anything. You will earn everything you learn in the "Cyber" field, mostly because you will spend hundred of hours reading, typing, learning. Also, your certifications will require more upkeep and continued learning that most other professional fields, Army and Civilian. Just choose wisely and start building your capabilities now and go with it.