There are still severe performance issues in the Minecraft server. When only one player is logged on to the server and the player are in specific areas of the world we get this all the time:
[09:14:47] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5944ms behind, skipping 118 tick(s)
[09:15:04] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4674ms behind, skipping 93 tick(s)
[09:15:21] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5025ms behind, skipping 100 tick(s)
[09:15:34] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3079ms behind, skipping 61 tick(s)
[09:15:53] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4481ms behind, skipping 89 tick(s)
[09:16:10] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3751ms behind, skipping 75 tick(s)
[09:16:24] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 2267ms behind, skipping 45 tick(s)
[09:16:44] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5615ms behind, skipping 112 tick(s)

Looking at the server load on an Ubuntu computer:
$ top -b -n 1 -d 10 -H | head -n 10
top - 09:18:02 up 40 days, 15:26, 3 users, load average: 1,00, 1,03, 0,88
Threads: 393 total, 3 running, 390 sleeping, 0 stopped, 0 zombie
%Cpu(s): 4,8 us, 0,1 sy, 0,0 ni, 95,0 id, 0,1 wa, 0,0 hi, 0,0 si, 0,0 st
KiB Mem: 4148312 total, 3866188 used, 282124 free, 125132 buffers
KiB Swap: 4192252 total, 213360 used, 3978892 free. 1179356 cached Mem

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
30031 ne 20 0 2512884 2,218g 10744 R 98,9 56,1 1647:03 java
22266 ne 20 0 6784 2988 2532 R 6,2 0,1 0:00.01 top
30037 ne 20 0 2512884 2,218g 10744 S 6,2 56,1 5:54.50 java

The server thread is running at maximum of what the CPU can handle. This was not the case in 1.8.

The world can be downloaded here (1.5GB zip file):
https://drive.google.com/file/d/0B4TrJIjkwdYzdE16ZUp5UngtZlU/view?usp=sharing

A suitable spot to be at: /tp -140 100 740

Compared to 1.8 this is a huge performance drop. You may argue that we should have a faster CPU, but when the load was at 25% in 1.8 I cannot see that this performance drop is reasonable.

CPU on Ubuntu computer: Pentium(R) Dual-Core CPU E6600 @ 3.06GHz
CPU on Windows 10 computer: Intel Core i7-2600 @ 3.40GHz

The problem is the same on both these computers. Both computers are equipped with SSD disc.