What tools and practices have you found effective when evaluating and changing your software engineering team structure (organization design)?

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Global Chief Cybersecurity Strategist & CISO in Healthcare and Biotech, Self-employed
Really depends upon your sector, size, stage of company. If tech then can look at what other like size successful companies have done. As an example, for Jeff Bezos a team size should be 7 +/- 3, or as he calls it “The two-pizza size rule”. If you can’t feed the team on two pizzas, the team is too big.
VP of Engineering in Services (non-Government), 1,001 - 5,000 employees
For evaluation :
- Surveys work well, no reason to re-evaluate if everything works well. But if people keep complaining about things like :
- Blurry reporting lines
- Lack of clear roles and responsibilities
- Too many dependencies
- Too many bottlenecks
- Slow decision making
- Too wide or too narrow span of control
You know that you have in front of yourself some reorganization to do

Then for changing this is a whole other beast. Change management is extremely complex as re-orgs often impacts people safety directly.
By safety I mean : role, title, scope of responsibility, area of influence, direct line manager etc..

So better involve the key people (that you have identified) as early as possible, to help you draft and drive the re-org. 
A mistake would be to have the transition long and smooth so people can slowly adjust, this would actually make the situation worst. Same as removing a bandaid very slowly.
So the speed of change will also have to be carefully controlled

Chief of DevOps and Partner in Healthcare and Biotech, 1,001 - 5,000 employees
I can highly recommend to use value stream identification and value stream mapping. 
Senior Director Engineering in Travel and Hospitality, 10,001+ employees
I would share a completely tangential view here. 
There are 2 ways really, outcome driven or people driven. 
If you have a leader who is great, create a team around the person. The structure doesnt really matter, but what matters is the flexibility and control you give to the leader.
If thats not an option, leverage standard team structures/hierarchies which are prevalent in the industry/ecosystem the company is in. This helps in attracting, retaining talent and reduces the amount of effort that needs to go in in educating the structure itself!
Chief Technology Officer in Software, 11 - 50 employees
Whilst I have never heard it put like that  has basically put in the most simple terms exactly how we operate. Love this 2 Pizza rule!!

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CTO in Software, 201 - 500 employees
Without a doubt - Technical Debt! It's a ball and chain that creates an ever increasing drag on any organization, stifles innovation, and prevents transformation.
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